[{"day":"01","publication":"Evolution","status":"public","doi":"10.1111/j.1558-5646.2009.00853.x","issue":"3","date_created":"2018-12-11T11:55:32Z","year":"2010","quality_controlled":0,"citation":{"apa":"Mank, J., Vicoso, B., Berlin, S., &#38; Charlesworth, B. (2010). Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>","chicago":"Mank, Judith, Beatriz Vicoso, Sofia Berlin, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>.","mla":"Mank, Judith, et al. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>, vol. 64, no. 3, Wiley-Blackwell, 2010, pp. 663–74, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>.","short":"J. Mank, B. Vicoso, S. Berlin, B. Charlesworth, Evolution 64 (2010) 663–674.","ieee":"J. Mank, B. Vicoso, S. Berlin, and B. Charlesworth, “Effective population size and the Faster-X effect: Empirical results and their interpretation,” <i>Evolution</i>, vol. 64, no. 3. Wiley-Blackwell, pp. 663–674, 2010.","ama":"Mank J, Vicoso B, Berlin S, Charlesworth B. Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. 2010;64(3):663-674. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>","ista":"Mank J, Vicoso B, Berlin S, Charlesworth B. 2010. Effective population size and the Faster-X effect: Empirical results and their interpretation. Evolution. 64(3), 663–674."},"_id":"2071","publist_id":"4967","acknowledgement":"We gratefully acknowledge funding from the Royal Society (to JEM)","type":"journal_article","volume":64,"author":[{"full_name":"Mank, Judith E","last_name":"Mank","first_name":"Judith"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","last_name":"Vicoso","first_name":"Beatriz"},{"last_name":"Berlin","first_name":"Sofia","full_name":"Berlin, Sofia"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"intvolume":"        64","extern":1,"date_updated":"2021-01-12T06:55:07Z","publisher":"Wiley-Blackwell","date_published":"2010-03-01T00:00:00Z","month":"03","title":"Effective population size and the Faster-X effect: Empirical results and their interpretation","publication_status":"published","abstract":[{"text":"The X or Z chromosome has several characteristics that distinguish it from the autosomes, namely hemizygosity in the heterogametic sex, and a potentially different effective population size, both of which may influence the rate and nature of evolution. In particular, there may be an accelerated rate of adaptive change for X-linked compared to autosomal coding sequences, often referred to as the Faster-X effect. Empirical studies have indicated that the strength of Faster-X evolution varies among different species, and theoretical treatments have shown that demography and mating system can substantially affect the degree of Faster-X evolution. Here we integrate genomic data on Faster-X evolution from a variety of animals with the demographic factors, mating system, and sex chromosome regulatory characteristics that may influence it. Our results suggest that differences in effective population size and mechanisms of dosage compensation may influence the perceived extent of Faster-X evolution, and help to explain several clade-specific patterns that we observe.","lang":"eng"}],"page":"663 - 674"},{"type":"dissertation","volume":499,"extern":1,"author":[{"last_name":"Bickel","first_name":"Bernd","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       499","_id":"2075","publist_id":"4963","abstract":[{"lang":"eng","text":"This thesis investigates the combination of data-driven and physically based techniques for acquiring, modeling, and animating deformable materials, with a special focus on human faces. Furthermore, based on these techniques, we introduce a data-driven process for designing and fabricating materials with desired deformation behavior. \nRealistic simulation behavior, surface details, and appearance are still demanding tasks. Neither pure data-driven, pure procedural, nor pure physical methods are best suited for accurate synthesis of facial motion and details (both for appearance and geometry), due to the difficulties in model design, parameter estimation, and desired controllability for animators. Capturing of a small but representative amount of real data, and then synthesizing diverse on-demand examples with physically-based models and real data as input benefits from both sides: Highly realistic model behavior due to real-world data and controllability due to physically-based models.\nTo model the face and its behavior, hybrid physically-based and data-driven approaches are elaborated. We investigate surface-based representations as well as a solid representation based on FEM. To achieve realistic behavior, we propose to build light-weighted data capture devices to acquire real-world data to estimate model parameters and to employ concepts from data-driven modeling techniques and machine learning. The resulting models support simple acquisition systems, offer techniques to process and extract model parameters from real-world data, provide a compact representation of the facial geometry and its motion, and allow intuitive editing. We demonstrate applications such as capture of facial geometry and motion and real-time animation and transfer of facial details, and show that our soft tissue model can react to external forces and produce realistic deformations beyond facial expressions.\nBased on this model, we furthermore introduce a data-driven process for designing and fabricating materials with desired deformation behavior. The process starts with measuring deformation properties of base materials. Each material is represented as a non-linear stress-strain relationship in a finite-element model. For material design and fabrication, we introduce an optimization process that finds the best combination of base materials that meets a user’s criteria specified by example deformations. Our algorithm employs a number of strategies to prune poor solutions from the combinatorial search space. We finally demonstrate the complete process by designing and fabricating objects with complex heterogeneous materials using modern multi-material 3D printers.\n"}],"publication_status":"published","publisher":"Unknown","date_updated":"2021-01-12T06:55:09Z","title":"Measurement-based modeling and fabrication of deformable materials for human faces","month":"01","date_published":"2010-01-01T00:00:00Z","year":"2010","date_created":"2018-12-11T11:55:34Z","publication":"Unknown","day":"01","status":"public","issue":"7458","doi":"dx.doi.org/10.3929/ethz-a-006354908","quality_controlled":0,"citation":{"ieee":"B. Bickel, “Measurement-based modeling and fabrication of deformable materials for human faces,” Unknown, 2010.","short":"B. Bickel, Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces, Unknown, 2010.","ista":"Bickel B. 2010. Measurement-based modeling and fabrication of deformable materials for human faces. Unknown.","ama":"Bickel B. Measurement-based modeling and fabrication of deformable materials for human faces. <i>Unknown</i>. 2010;499(7458). doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>","apa":"Bickel, B. (2010). <i>Measurement-based modeling and fabrication of deformable materials for human faces</i>. <i>Unknown</i>. Unknown. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>","chicago":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>. Unknown, 2010. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>.","mla":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>, vol. 499, no. 7458, Unknown, 2010, doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>."}},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"extern":"1","volume":7,"article_processing_charge":"No","page":"1874-1878","external_id":{"arxiv":["1010.2453"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results."}],"keyword":["condensed matter physics","general chemistry"],"title":"Particle self-assembly on soft elastic shells","date_created":"2021-10-12T08:34:23Z","year":"2010","publication_identifier":{"issn":["1744-683X","1744-6848"]},"doi":"10.1039/c0sm01143f","issue":"5","publication":"Soft Matter","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1010.2453","open_access":"1"}],"intvolume":"         7","oa_version":"Preprint","article_type":"original","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.","type":"journal_article","_id":"10127","oa":1,"date_published":"2010-12-23T00:00:00Z","language":[{"iso":"eng"}],"month":"12","date_updated":"2021-10-12T09:49:27Z","publisher":"Royal Society of Chemistry (RSC)","arxiv":1,"status":"public","day":"23","citation":{"mla":"Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” <i>Soft Matter</i>, vol. 7, no. 5, Royal Society of Chemistry (RSC), 2010, pp. 1874–78, doi:<a href=\"https://doi.org/10.1039/c0sm01143f\">10.1039/c0sm01143f</a>.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” <i>Soft Matter</i>. Royal Society of Chemistry (RSC), 2010. <a href=\"https://doi.org/10.1039/c0sm01143f\">https://doi.org/10.1039/c0sm01143f</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2010). Particle self-assembly on soft elastic shells. <i>Soft Matter</i>. Royal Society of Chemistry (RSC). <a href=\"https://doi.org/10.1039/c0sm01143f\">https://doi.org/10.1039/c0sm01143f</a>","ama":"Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. <i>Soft Matter</i>. 2010;7(5):1874-1878. doi:<a href=\"https://doi.org/10.1039/c0sm01143f\">10.1039/c0sm01143f</a>","ista":"Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells. Soft Matter. 7(5), 1874–1878.","short":"A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878.","ieee":"A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,” <i>Soft Matter</i>, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878, 2010."}},{"main_file_link":[{"url":"https://europepmc.org/article/med/20428547"}],"quality_controlled":"1","publication":"Physical Chemistry Chemical Physics","publication_identifier":{"issn":["1463-9076","1463-9084"]},"doi":"10.1039/b923041f","issue":"18","date_created":"2021-10-12T08:44:34Z","year":"2010","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"title":"Quantum mechanical study of secondary structure formation in protected dipeptides","publication_status":"published","external_id":{"pmid":["20428547"]},"abstract":[{"lang":"eng","text":"An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand."}],"article_processing_charge":"No","page":"4678-4685","pmid":1,"volume":12,"author":[{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Hrenar, T.","first_name":"T.","last_name":"Hrenar"},{"full_name":"Mališ, M.","last_name":"Mališ","first_name":"M."},{"full_name":"Došlić, N.","last_name":"Došlić","first_name":"N."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"mla":"Šarić, Anđela, et al. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” <i>Physical Chemistry Chemical Physics</i>, vol. 12, no. 18, Royal Society of Chemistry , 2010, pp. 4678–85, doi:<a href=\"https://doi.org/10.1039/b923041f\">10.1039/b923041f</a>.","chicago":"Šarić, Anđela, T. Hrenar, M. Mališ, and N. Došlić. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry , 2010. <a href=\"https://doi.org/10.1039/b923041f\">https://doi.org/10.1039/b923041f</a>.","apa":"Šarić, A., Hrenar, T., Mališ, M., &#38; Došlić, N. (2010). Quantum mechanical study of secondary structure formation in protected dipeptides. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/b923041f\">https://doi.org/10.1039/b923041f</a>","ama":"Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. <i>Physical Chemistry Chemical Physics</i>. 2010;12(18):4678-4685. doi:<a href=\"https://doi.org/10.1039/b923041f\">10.1039/b923041f</a>","ista":"Šarić A, Hrenar T, Mališ M, Došlić N. 2010. Quantum mechanical study of secondary structure formation in protected dipeptides. Physical Chemistry Chemical Physics. 12(18), 4678–4685.","ieee":"A. Šarić, T. Hrenar, M. Mališ, and N. Došlić, “Quantum mechanical study of secondary structure formation in protected dipeptides,” <i>Physical Chemistry Chemical Physics</i>, vol. 12, no. 18. Royal Society of Chemistry , pp. 4678–4685, 2010.","short":"A. Šarić, T. Hrenar, M. Mališ, N. Došlić, Physical Chemistry Chemical Physics 12 (2010) 4678–4685."},"status":"public","day":"16","date_updated":"2021-10-12T09:49:22Z","publisher":"Royal Society of Chemistry ","date_published":"2010-03-16T00:00:00Z","month":"03","language":[{"iso":"eng"}],"_id":"10128","acknowledgement":"This work has been supported by the MZOŠ projects 098-0352851-2921 and 119-1191342-2959.","type":"journal_article","oa_version":"None","intvolume":"        12","article_type":"original"},{"scopus_import":"1","_id":"10390","intvolume":"       115","oa_version":"Preprint","article_type":"original","type":"journal_article","acknowledgement":"This work was supported by the National Science Foundation under CAREER Grant No. DMR-0846426 and partly by Columbia University.","date_published":"2010-10-15T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2021-11-29T16:20:29Z","publisher":"American Chemical Society","arxiv":1,"oa":1,"status":"public","day":"15","citation":{"mla":"Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” <i>The Journal of Physical Chemistry B</i>, vol. 115, no. 22, American Chemical Society, 2010, pp. 7182–89, doi:<a href=\"https://doi.org/10.1021/jp107545w\">10.1021/jp107545w</a>.","apa":"Šarić, A., Bozorgui, B., &#38; Cacciuto, A. (2010). Packing of soft asymmetric dumbbells. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp107545w\">https://doi.org/10.1021/jp107545w</a>","chicago":"Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric Dumbbells.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/jp107545w\">https://doi.org/10.1021/jp107545w</a>.","ista":"Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 115(22), 7182–7189.","ama":"Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. <i>The Journal of Physical Chemistry B</i>. 2010;115(22):7182-7189. doi:<a href=\"https://doi.org/10.1021/jp107545w\">10.1021/jp107545w</a>","ieee":"A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,” <i>The Journal of Physical Chemistry B</i>, vol. 115, no. 22. American Chemical Society, pp. 7182–7189, 2010.","short":"A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115 (2010) 7182–7189."},"pmid":1,"author":[{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Bozorgui","first_name":"Behnaz","full_name":"Bozorgui, Behnaz"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","volume":115,"keyword":["materials chemistry"],"title":"Packing of soft asymmetric dumbbells","article_processing_charge":"No","page":"7182-7189","publication_status":"published","external_id":{"pmid":["20949934"],"arxiv":["1010.2458"]},"abstract":[{"text":"We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration.","lang":"eng"}],"doi":"10.1021/jp107545w","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"issue":"22","publication":"The Journal of Physical Chemistry B","date_created":"2021-11-29T15:13:17Z","year":"2010","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1010.2458"}],"quality_controlled":"1"},{"status":"public","day":"03","citation":{"mla":"Šarić, Anđela, et al. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” <i>Physical Review Letters</i>, vol. 104, no. 22, 226101, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.226101\">10.1103/physrevlett.104.226101</a>.","chicago":"Šarić, Anđela, Josep C. Pàmies, and Angelo Cacciuto. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.226101\">https://doi.org/10.1103/physrevlett.104.226101</a>.","apa":"Šarić, A., Pàmies, J. C., &#38; Cacciuto, A. (2010). Effective elasticity of a flexible filament bound to a deformable cylindrical surface. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.226101\">https://doi.org/10.1103/physrevlett.104.226101</a>","ista":"Šarić A, Pàmies JC, Cacciuto A. 2010. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. Physical Review Letters. 104(22), 226101.","ama":"Šarić A, Pàmies JC, Cacciuto A. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. <i>Physical Review Letters</i>. 2010;104(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.226101\">10.1103/physrevlett.104.226101</a>","ieee":"A. Šarić, J. C. Pàmies, and A. Cacciuto, “Effective elasticity of a flexible filament bound to a deformable cylindrical surface,” <i>Physical Review Letters</i>, vol. 104, no. 22. American Physical Society, 2010.","short":"A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010)."},"acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.","type":"journal_article","intvolume":"       104","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"10391","oa":1,"date_updated":"2021-11-30T08:11:19Z","arxiv":1,"publisher":"American Physical Society","date_published":"2010-06-03T00:00:00Z","month":"06","language":[{"iso":"eng"}],"article_number":"226101","date_created":"2021-11-29T15:14:33Z","year":"2010","publication":"Physical Review Letters","doi":"10.1103/physrevlett.104.226101","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"issue":"22","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1005.2429","open_access":"1"}],"volume":104,"author":[{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Pàmies, Josep C.","last_name":"Pàmies","first_name":"Josep C."},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","pmid":1,"publication_status":"published","external_id":{"arxiv":["1005.2429"],"pmid":["20867183"]},"abstract":[{"text":"We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results.","lang":"eng"}],"article_processing_charge":"No","keyword":["general physics and astronomy"],"title":"Effective elasticity of a flexible filament bound to a deformable cylindrical surface"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Mark, Manfred","last_name":"Mark","first_name":"Manfred"},{"full_name":"Haller, Elmar","first_name":"Elmar","last_name":"Haller"},{"last_name":"Gustavsson","first_name":"Mattias","full_name":"Gustavsson, Mattias"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"full_name":"Nägerl, Hanns","first_name":"Hanns","last_name":"Nägerl"}],"oa_version":"None","extern":"1","type":"conference","publist_id":"6346","_id":"1042","article_processing_charge":"No","page":"256 - 269","publication_status":"published","abstract":[{"text":"Recent years have seen tremendous progress in the field of cold and ultracold molecules. A central goal in the field is currently the realization of stable rovibronic ground-state molecular samples in the regime of quantum degeneracy, e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate Fermi gases, or, when an optical lattice is present, molecular Mott-insulator phases. However, molecular samples are not readily cooled to the extremely low temperatures at which quantum degeneracy occurs. In particular, laser cooling, the \\'workhorse\\' for the field of atomic quantum gases, is generally not applicable to molecular samples. Here we take an important step beyond previous work1 and provide details on the realization of an ultracold quantum gas of ground-state dimer molecules trapped in an optical lattice as recently reported in Ref. 2. We demonstrate full control over all internal and external quantum degrees of freedom for the ground-state molecules by deterministically preparing the molecules in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic ground state, while the molecules are trapped in the motional ground state of the individual lattice wells. We circumvent the problem of cooling by associating weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and by transferring these to the absolute ground state in a four-photon STIRAP process. Our preparation procedure directly leads to a long-lived, lattice-trapped molecular many-body state, which we expect to form the platform for many of the envisioned future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy, quantum information science, and dipolar quantum systems.","lang":"eng"}],"date_published":"2010-01-01T00:00:00Z","month":"01","language":[{"iso":"eng"}],"title":"Production of a quantum gas of rovibronic ground-state molecules in an optical lattice","date_updated":"2021-01-12T06:47:52Z","publisher":"World Scientific Publishing","date_created":"2018-12-11T11:49:50Z","year":"2010","doi":"10.1142/9789814282345_0024","status":"public","day":"01","citation":{"ista":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. 2010. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. ICOLS: International Conference on Laser Spectroscopy, 256–269.","ama":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. In: World Scientific Publishing; 2010:256-269. doi:<a href=\"https://doi.org/10.1142/9789814282345_0024\">10.1142/9789814282345_0024</a>","ieee":"J. G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and H. Nägerl, “Production of a quantum gas of rovibronic ground-state molecules in an optical lattice,” presented at the ICOLS: International Conference on Laser Spectroscopy, 2010, pp. 256–269.","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, H. Nägerl, in:, World Scientific Publishing, 2010, pp. 256–269.","mla":"Danzl, Johann G., et al. <i>Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice</i>. World Scientific Publishing, 2010, pp. 256–69, doi:<a href=\"https://doi.org/10.1142/9789814282345_0024\">10.1142/9789814282345_0024</a>.","chicago":"Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Hanns Nägerl. “Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice,” 256–69. World Scientific Publishing, 2010. <a href=\"https://doi.org/10.1142/9789814282345_0024\">https://doi.org/10.1142/9789814282345_0024</a>.","apa":"Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., &#38; Nägerl, H. (2010). Production of a quantum gas of rovibronic ground-state molecules in an optical lattice (pp. 256–269). Presented at the ICOLS: International Conference on Laser Spectroscopy, World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789814282345_0024\">https://doi.org/10.1142/9789814282345_0024</a>"},"conference":{"name":"ICOLS: International Conference on Laser Spectroscopy"}},{"date_created":"2018-12-11T11:49:51Z","year":"2010","publication":"Nature Physics","doi":"10.1038/nphys1533","issue":"4","main_file_link":[{"url":"https://arxiv.org/abs/0909.4700","open_access":"1"}],"volume":6,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Mark, Manfred","last_name":"Mark","first_name":"Manfred"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"last_name":"Gustavsson","first_name":"Mattias","full_name":"Gustavsson, Mattias"},{"last_name":"Hart","first_name":"Russell","full_name":"Hart, Russell"},{"last_name":"Aldegunde","first_name":"Jesus","full_name":"Aldegunde, Jesus"},{"full_name":"Hutson, Jeremy","first_name":"Jeremy","last_name":"Hutson"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}],"extern":"1","external_id":{"arxiv":["0909.4700"]},"publication_status":"published","abstract":[{"text":"Control over all internal and external degrees of freedom of molecules at the level of single quantum states will enable a series of fundamental studies in physics and chemistry1,2. In particular, samples of ground-state molecules at ultralow temperatures and high number densities will facilitate new quantum-gas studies3 and future applications in quantum information science4. However, high phase-space densities for molecular samples are not readily attainable because efficient cooling techniques such as laser cooling are lacking. Here we produce an ultracold and dense sample of molecules in a single hyperfine level of the rovibronic ground state with each molecule individually trapped in the motional ground state of an optical lattice well. Starting from a zero-temperature atomic Mott-insulator state with optimized double-site occupancy6, weakly bound dimer molecules are efficiently associated on a Feshbach resonance7 and subsequently transferred to the rovibronic ground state by a stimulated four-photon process with &gt;50% efficiency. The molecules are trapped in the lattice and have a lifetime of 8 s. Our results present a crucial step towards Bose-Einstein condensation of ground-state molecules and, when suitably generalized to polar heteronuclear molecules, the realization of dipolar quantum-gas phases in optical lattices8-10.","lang":"eng"}],"article_processing_charge":"No","page":"265 - 270","title":"An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice","status":"public","day":"04","citation":{"ista":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Aldegunde J, Hutson J, Nägerl H. 2010. An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice. Nature Physics. 6(4), 265–270.","ama":"Danzl JG, Mark M, Haller E, et al. An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice. <i>Nature Physics</i>. 2010;6(4):265-270. doi:<a href=\"https://doi.org/10.1038/nphys1533\">10.1038/nphys1533</a>","ieee":"J. G. Danzl <i>et al.</i>, “An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice,” <i>Nature Physics</i>, vol. 6, no. 4. Nature Publishing Group, pp. 265–270, 2010.","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J. Aldegunde, J. Hutson, H. Nägerl, Nature Physics 6 (2010) 265–270.","mla":"Danzl, Johann G., et al. “An Ultracold High-Density Sample of Rovibronic Ground-State Molecules in an Optical Lattice.” <i>Nature Physics</i>, vol. 6, no. 4, Nature Publishing Group, 2010, pp. 265–70, doi:<a href=\"https://doi.org/10.1038/nphys1533\">10.1038/nphys1533</a>.","chicago":"Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, Jesus Aldegunde, Jeremy Hutson, and Hanns Nägerl. “An Ultracold High-Density Sample of Rovibronic Ground-State Molecules in an Optical Lattice.” <i>Nature Physics</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nphys1533\">https://doi.org/10.1038/nphys1533</a>.","apa":"Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Aldegunde, J., … Nägerl, H. (2010). An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys1533\">https://doi.org/10.1038/nphys1533</a>"},"acknowledgement":"We thank H. Ritsch, S. Dürr, N. Bouloufa and O. Dulieu for valuable discussions. We are indebted to R. Grimm for generous support and to H. Häffner for the loan of a charge-coupled camera. We gratefully acknowledge financial support by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant and by the European Science Foundation within the framework of the EuroQUASAR collective research project QuDeGPM and within the framework of the EuroQUAM collective research project QuDipMol. R.H. is supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.","type":"journal_article","oa_version":"Preprint","intvolume":"         6","_id":"1044","publist_id":"6345","oa":1,"date_updated":"2021-01-12T06:47:53Z","arxiv":1,"publisher":"Nature Publishing Group","date_published":"2010-04-04T00:00:00Z","language":[{"iso":"eng"}],"month":"04"},{"publication":"Physical Review Letters","issue":"15","doi":"10.1103/PhysRevLett.104.153203","year":"2010","date_created":"2018-12-11T11:49:51Z","main_file_link":[{"url":"https://arxiv.org/abs/1002.3795","open_access":"1"}],"volume":104,"extern":"1","author":[{"first_name":"Elmar","last_name":"Haller","full_name":"Haller, Elmar"},{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"last_name":"Hart","first_name":"Russell","full_name":"Hart, Russell"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Reichsöllner, Lukas","last_name":"Reichsöllner","first_name":"Lukas"},{"first_name":"Vladimir","last_name":"Melezhik","full_name":"Melezhik, Vladimir"},{"full_name":"Schmelcher, Peter","first_name":"Peter","last_name":"Schmelcher"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Confinement-induced resonances in low-dimensional quantum systems","abstract":[{"lang":"eng","text":"We report on the observation of confinement-induced resonances in strongly interacting quantum-gas systems with tunable interactions for one- and two-dimensional geometry. Atom-atom scattering is substantially modified when the s-wave scattering length approaches the length scale associated with the tight transversal confinement, leading to characteristic loss and heating signatures. Upon introducing an anisotropy for the transversal confinement we observe a splitting of the confinement-induced resonance. With increasing anisotropy additional resonances appear. In the limit of a two-dimensional system we find that one resonance persists."}],"external_id":{"arxiv":["1002.3795"]},"publication_status":"published","article_processing_charge":"No","day":"14","status":"public","citation":{"mla":"Haller, Elmar, et al. “Confinement-Induced Resonances in Low-Dimensional Quantum Systems.” <i>Physical Review Letters</i>, vol. 104, no. 15, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.153203\">10.1103/PhysRevLett.104.153203</a>.","chicago":"Haller, Elmar, Manfred Mark, Russell Hart, Johann G Danzl, Lukas Reichsöllner, Vladimir Melezhik, Peter Schmelcher, and Hanns Nägerl. “Confinement-Induced Resonances in Low-Dimensional Quantum Systems.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.153203\">https://doi.org/10.1103/PhysRevLett.104.153203</a>.","apa":"Haller, E., Mark, M., Hart, R., Danzl, J. G., Reichsöllner, L., Melezhik, V., … Nägerl, H. (2010). Confinement-induced resonances in low-dimensional quantum systems. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.153203\">https://doi.org/10.1103/PhysRevLett.104.153203</a>","ama":"Haller E, Mark M, Hart R, et al. Confinement-induced resonances in low-dimensional quantum systems. <i>Physical Review Letters</i>. 2010;104(15). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.153203\">10.1103/PhysRevLett.104.153203</a>","ista":"Haller E, Mark M, Hart R, Danzl JG, Reichsöllner L, Melezhik V, Schmelcher P, Nägerl H. 2010. Confinement-induced resonances in low-dimensional quantum systems. Physical Review Letters. 104(15).","ieee":"E. Haller <i>et al.</i>, “Confinement-induced resonances in low-dimensional quantum systems,” <i>Physical Review Letters</i>, vol. 104, no. 15. American Physical Society, 2010.","short":"E. Haller, M. Mark, R. Hart, J.G. Danzl, L. Reichsöllner, V. Melezhik, P. Schmelcher, H. Nägerl, Physical Review Letters 104 (2010)."},"_id":"1045","publist_id":"6344","type":"journal_article","acknowledgement":"We thank W. Zwerger for discussions and R. Grimm for generous support. We acknowledge funding by the Austrian Science Fund and by the European Union within the framework of the EuroQUASAR collective research project QuDeGPM. R. H. is supported by a Marie Curie Fellowship within FP7. P. S. acknowledges financial support by the DFG. Financial support by the Heisenberg-Landau Program is appreciated by P. S. and V. M.","oa_version":"Preprint","intvolume":"       104","arxiv":1,"publisher":"American Physical Society","date_updated":"2021-01-12T06:47:53Z","language":[{"iso":"eng"}],"month":"04","date_published":"2010-04-14T00:00:00Z","oa":1},{"date_created":"2018-12-11T11:49:51Z","year":"2010","day":"28","status":"public","publication":"New Journal of Physics","doi":"10.1088/1367-2630/12/6/065029","citation":{"ieee":"M. Gustavsson <i>et al.</i>, “Interference of interacting matter waves,” <i>New Journal of Physics</i>, vol. 12. IOP Publishing Ltd., 2010.","short":"M. Gustavsson, E. Haller, M. Mark, J.G. Danzl, R. Hart, A. Daley, H. Nägerl, New Journal of Physics 12 (2010).","ama":"Gustavsson M, Haller E, Mark M, et al. Interference of interacting matter waves. <i>New Journal of Physics</i>. 2010;12. doi:<a href=\"https://doi.org/10.1088/1367-2630/12/6/065029\">10.1088/1367-2630/12/6/065029</a>","ista":"Gustavsson M, Haller E, Mark M, Danzl JG, Hart R, Daley A, Nägerl H. 2010. Interference of interacting matter waves. New Journal of Physics. 12.","chicago":"Gustavsson, Mattias, Elmar Haller, Manfred Mark, Johann G Danzl, Russell Hart, Andrew Daley, and Hanns Nägerl. “Interference of Interacting Matter Waves.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2010. <a href=\"https://doi.org/10.1088/1367-2630/12/6/065029\">https://doi.org/10.1088/1367-2630/12/6/065029</a>.","apa":"Gustavsson, M., Haller, E., Mark, M., Danzl, J. G., Hart, R., Daley, A., &#38; Nägerl, H. (2010). Interference of interacting matter waves. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/12/6/065029\">https://doi.org/10.1088/1367-2630/12/6/065029</a>","mla":"Gustavsson, Mattias, et al. “Interference of Interacting Matter Waves.” <i>New Journal of Physics</i>, vol. 12, IOP Publishing Ltd., 2010, doi:<a href=\"https://doi.org/10.1088/1367-2630/12/6/065029\">10.1088/1367-2630/12/6/065029</a>."},"acknowledgement":"We thank E Arimondo, O Morsch, W Schleich, A Smerzi, D Witthaut and A Buchleitner and his group for helpful discussions. We also thank R Grimm for generous support. We gratefully acknowledge funding from the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant and through SFB 15. RH is supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.","type":"journal_article","volume":12,"intvolume":"        12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","author":[{"full_name":"Gustavsson, Mattias","first_name":"Mattias","last_name":"Gustavsson"},{"first_name":"Elmar","last_name":"Haller","full_name":"Haller, Elmar"},{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hart","first_name":"Russell","full_name":"Hart, Russell"},{"first_name":"Andrew","last_name":"Daley","full_name":"Daley, Andrew"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"extern":"1","_id":"1046","publist_id":"6342","publication_status":"published","abstract":[{"lang":"eng","text":"The phenomenon of matter-wave interference lies at the heart of quantum physics. It has been observed in various contexts in the limit of non-interacting particles as a single-particle effect. Here we observe and control matter-wave interference whose evolution is driven by interparticle interactions. In a multi-path matter-wave interferometer, the macroscopic manybody wave function of an interacting atomic Bose-Einstein condensate develops a regular interference pattern, allowing us to detect and directly visualize the effect of interaction-induced phase shifts. We demonstrate control over the phase evolution by inhibiting interaction-induced dephasing and by refocusing a dephased macroscopic matter wave in a spin-echo-type experiment. Our results show that interactions in a many-body system lead to a surprisingly coherent evolution, possibly enabling narrow-band and high-brightness matterwave interferometers based on atom lasers."}],"article_processing_charge":"No","date_updated":"2021-01-12T06:47:53Z","publisher":"IOP Publishing Ltd.","date_published":"2010-06-28T00:00:00Z","language":[{"iso":"eng"}],"title":"Interference of interacting matter waves","month":"06"},{"oa":1,"language":[{"iso":"eng"}],"month":"05","date_published":"2010-05-21T00:00:00Z","arxiv":1,"publisher":"American Physical Society","date_updated":"2021-01-12T06:47:54Z","intvolume":"       104","oa_version":"Preprint","acknowledgement":"We thank A. R. Kolovsky, A. Zenesini, and A. Wacker for discussions and R. Grimm for generous support. We acknowledge funding by the Austrian Ministry of Science and Research and the Austrian Science Fund and by the European Union within the framework of the EuroQUASAR collective research project QuDeGPM. R. H. is supported by a Marie Curie Action within FP7.","type":"journal_article","publist_id":"6343","_id":"1047","citation":{"apa":"Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., &#38; Nägerl, H. (2010). Inducing transport in a dissipation-free lattice with super bloch oscillations. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">https://doi.org/10.1103/PhysRevLett.104.200403</a>","chicago":"Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner, and Hanns Nägerl. “Inducing Transport in a Dissipation-Free Lattice with Super Bloch Oscillations.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">https://doi.org/10.1103/PhysRevLett.104.200403</a>.","mla":"Haller, Elmar, et al. “Inducing Transport in a Dissipation-Free Lattice with Super Bloch Oscillations.” <i>Physical Review Letters</i>, vol. 104, no. 20, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">10.1103/PhysRevLett.104.200403</a>.","short":"E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical Review Letters 104 (2010).","ieee":"E. Haller, R. Hart, M. Mark, J. G. Danzl, L. Reichsöllner, and H. Nägerl, “Inducing transport in a dissipation-free lattice with super bloch oscillations,” <i>Physical Review Letters</i>, vol. 104, no. 20. American Physical Society, 2010.","ista":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. 2010. Inducing transport in a dissipation-free lattice with super bloch oscillations. Physical Review Letters. 104(20).","ama":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Nägerl H. Inducing transport in a dissipation-free lattice with super bloch oscillations. <i>Physical Review Letters</i>. 2010;104(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.200403\">10.1103/PhysRevLett.104.200403</a>"},"day":"21","status":"public","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Particles in a perfect lattice potential perform Bloch oscillations when subject to a constant force, leading to localization and preventing conductivity. For a weakly interacting Bose-Einstein condensate of Cs atoms, we observe giant center-of-mass oscillations in position space with a displacement across hundreds of lattice sites when we add a periodic modulation to the force near the Bloch frequency. We study the dependence of these &quot;super&quot; Bloch oscillations on lattice depth, modulation amplitude, and modulation frequency and show that they provide a means to induce linear transport in a dissipation-free lattice."}],"publication_status":"published","external_id":{"arxiv":["1001.1206"]},"title":"Inducing transport in a dissipation-free lattice with super bloch oscillations","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Reichsöllner, Lukas","first_name":"Lukas","last_name":"Reichsöllner"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"volume":104,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1001.1206"}],"year":"2010","date_created":"2018-12-11T11:49:52Z","issue":"20","doi":"10.1103/PhysRevLett.104.200403","publication":"Physical Review Letters"},{"status":"public","day":"29","citation":{"ista":"Haller E, Hart R, Mark M, Danzl JG, Reichsöllner L, Gustavsson M, Dalmonte M, Pupillo G, Nägerl H. 2010. Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. Nature. 466(7306), 597–600.","ama":"Haller E, Hart R, Mark M, et al. Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. <i>Nature</i>. 2010;466(7306):597-600. doi:<a href=\"https://doi.org/10.1038/nature09259\">10.1038/nature09259</a>","ieee":"E. Haller <i>et al.</i>, “Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons,” <i>Nature</i>, vol. 466, no. 7306. Nature Publishing Group, pp. 597–600, 2010.","short":"E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, M. Gustavsson, M. Dalmonte, G. Pupillo, H. Nägerl, Nature 466 (2010) 597–600.","mla":"Haller, Elmar, et al. “Pinning Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.” <i>Nature</i>, vol. 466, no. 7306, Nature Publishing Group, 2010, pp. 597–600, doi:<a href=\"https://doi.org/10.1038/nature09259\">10.1038/nature09259</a>.","apa":"Haller, E., Hart, R., Mark, M., Danzl, J. G., Reichsöllner, L., Gustavsson, M., … Nägerl, H. (2010). Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09259\">https://doi.org/10.1038/nature09259</a>","chicago":"Haller, Elmar, Russell Hart, Manfred Mark, Johann G Danzl, Lukas Reichsöllner, Mattias Gustavsson, Marcello Dalmonte, Guido Pupillo, and Hanns Nägerl. “Pinning Quantum Phase Transition for a Luttinger Liquid of Strongly Interacting Bosons.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09259\">https://doi.org/10.1038/nature09259</a>."},"oa_version":"Preprint","intvolume":"       466","acknowledgement":"We thank W. Zwerger for discussions. We are indebted to R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant, and by the European Union through the STREP FP7-ICT-2007-C project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within the framework of the EuroQUASAR collective research project QuDeGPM. R.H. is supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.","type":"journal_article","publist_id":"6341","_id":"1049","oa":1,"month":"07","language":[{"iso":"eng"}],"date_published":"2010-07-29T00:00:00Z","arxiv":1,"publisher":"Nature Publishing Group","date_updated":"2021-01-12T06:47:54Z","year":"2010","date_created":"2018-12-11T11:49:52Z","issue":"7306","doi":"10.1038/nature09259","publication":"Nature","main_file_link":[{"url":"https://arxiv.org/abs/1004.3168","open_access":"1"}],"extern":"1","author":[{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"full_name":"Hart, Russell","first_name":"Russell","last_name":"Hart"},{"full_name":"Mark, Manfred","last_name":"Mark","first_name":"Manfred"},{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"full_name":"Reichsöllner, Lukas","first_name":"Lukas","last_name":"Reichsöllner"},{"full_name":"Gustavsson, Mattias","first_name":"Mattias","last_name":"Gustavsson"},{"full_name":"Dalmonte, Marcello","first_name":"Marcello","last_name":"Dalmonte"},{"first_name":"Guido","last_name":"Pupillo","full_name":"Pupillo, Guido"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":466,"page":"597 - 600","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Quantum many-body systems can have phase transitions even at zero temperature; fluctuations arising from Heisenbergĝ€™s uncertainty principle, as opposed to thermal effects, drive the system from one phase to another. Typically, during the transition the relative strength of two competing terms in the systemĝ€™s Hamiltonian changes across a finite critical value. A well-known example is the Mottĝ€&quot; Hubbard quantum phase transition from a superfluid to an insulating phase, which has been observed for weakly interacting bosonic atomic gases. However, for strongly interacting quantum systems confined to lower-dimensional geometry, a novel type of quantum phase transition may be induced and driven by an arbitrarily weak perturbation to the Hamiltonian. Here we observe such an effectĝ€&quot;the sineĝ€&quot;Gordon quantum phase transition from a superfluid Luttinger liquid to a Mott insulatorĝ€ &quot;in a one-dimensional quantum gas of bosonic caesium atoms with tunable interactions. For sufficiently strong interactions, the transition is induced by adding an arbitrarily weak optical lattice commensurate with the atomic granularity, which leads to immediate pinning of the atoms. We map out the phase diagram and find that our measurements in the strongly interacting regime agree well with a quantum field description based on the exactly solvable sineĝ€&quot;Gordon model. We trace the phase boundary all the way to the weakly interacting regime, where we find good agreement with the predictions of the one-dimensional Boseĝ€&quot;Hubbard model. Our results open up the experimental study of quantum phase transitions, criticality and transport phenomena beyond Hubbard-type models in the context of ultracold gases."}],"publication_status":"published","external_id":{"arxiv":["1004.3168"]},"title":"Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons"},{"date_published":"2010-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","title":"Brief announcement: New bounds for partially synchronous set agreement","date_updated":"2023-02-23T13:11:26Z","publisher":"Springer","article_processing_charge":"No","page":"404 - 405","publication_status":"published","abstract":[{"text":"Set agreement [4] is a fundamental problem in distributed computing, in which processes collectively choose a small subset of values from a larger set of proposals. Set agreement has been extensively studied in both synchronous and asynchronous systems [10,11,3,5,8,9]. Real world distributed systems, however, are neither purely synchronous nor purely asynchronous. To describe such a system, Dwork et al. [6] introduced the idea of partial synchrony. They assume for every execution some (unknown) time GST (global stabilization time), after which the system is synchronous. In a recent paper [1,2], we study the complexity of set agreement in the context of partially synchronous systems, determining the minimum-sized window of synchrony in which set agreement can be solved. We show that at least ⌊t/k⌋ + 2 synchronous rounds are required for k-set agreement, where t &lt; n is the number of crashes, and k is the agreement parameter of the set agreement task. We then introduce an algorithm that terminates in any window of synchrony of size at least ⌊t/k⌋ + 4 rounds. Together, these results tightly bound the inherent price of tolerating some asynchrony.","lang":"eng"}],"publist_id":"6899","_id":"758","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"},{"full_name":"Travers, Corentin","first_name":"Corentin","last_name":"Travers"}],"oa_version":"None","extern":"1","volume":"6343 LNCS","type":"conference","conference":{"name":"DISC: Distributed Computing"},"citation":{"ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Brief announcement: New bounds for partially synchronous set agreement,” presented at the DISC: Distributed Computing, 2010, vol. 6343 LNCS, pp. 404–405.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2010, pp. 404–405.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Brief announcement: New bounds for partially synchronous set agreement. In: Vol 6343 LNCS. Springer; 2010:404-405. doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_40\">10.1007/978-3-642-15763-9_40</a>","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2010. Brief announcement: New bounds for partially synchronous set agreement. DISC: Distributed Computing, LNCS, vol. 6343 LNCS, 404–405.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., &#38; Travers, C. (2010). Brief announcement: New bounds for partially synchronous set agreement (Vol. 6343 LNCS, pp. 404–405). Presented at the DISC: Distributed Computing, Springer. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_40\">https://doi.org/10.1007/978-3-642-15763-9_40</a>","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Brief Announcement: New Bounds for Partially Synchronous Set Agreement,” 6343 LNCS:404–5. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_40\">https://doi.org/10.1007/978-3-642-15763-9_40</a>.","mla":"Alistarh, Dan-Adrian, et al. <i>Brief Announcement: New Bounds for Partially Synchronous Set Agreement</i>. Vol. 6343 LNCS, Springer, 2010, pp. 404–05, doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_40\">10.1007/978-3-642-15763-9_40</a>."},"doi":"10.1007/978-3-642-15763-9_40","alternative_title":["LNCS"],"status":"public","day":"01","date_created":"2018-12-11T11:48:21Z","year":"2010"},{"issue":"5","doi":"10.1016/j.cell.2010.08.024","publication_identifier":{"issn":["0092-8674"]},"status":"public","publication":"Cell","day":"03","year":"2010","date_created":"2020-04-30T10:36:52Z","citation":{"mla":"Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.” <i>Cell</i>, vol. 142, no. 5, Elsevier, 2010, pp. 679–81, doi:<a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">10.1016/j.cell.2010.08.024</a>.","apa":"Sweeney, L. B., &#38; Luo, L. (2010). ‘Fore brain: A hint of the ancestral cortex. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">https://doi.org/10.1016/j.cell.2010.08.024</a>","chicago":"Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.” <i>Cell</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">https://doi.org/10.1016/j.cell.2010.08.024</a>.","ista":"Sweeney LB, Luo L. 2010. ‘Fore brain: A hint of the ancestral cortex. Cell. 142(5), 679–681.","ama":"Sweeney LB, Luo L. ‘Fore brain: A hint of the ancestral cortex. <i>Cell</i>. 2010;142(5):679-681. doi:<a href=\"https://doi.org/10.1016/j.cell.2010.08.024\">10.1016/j.cell.2010.08.024</a>","short":"L.B. Sweeney, L. Luo, Cell 142 (2010) 679–681.","ieee":"L. B. Sweeney and L. Luo, “‘Fore brain: A hint of the ancestral cortex,” <i>Cell</i>, vol. 142, no. 5. Elsevier, pp. 679–681, 2010."},"quality_controlled":"1","_id":"7703","extern":"1","article_type":"original","intvolume":"       142","author":[{"last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":142,"type":"journal_article","title":"‘Fore brain: A hint of the ancestral cortex","month":"09","language":[{"iso":"eng"}],"date_published":"2010-09-03T00:00:00Z","publisher":"Elsevier","date_updated":"2024-01-31T10:14:59Z","page":"679-681","article_processing_charge":"No","abstract":[{"text":"By combining gene expression profiling with image registration, Tomer et al. (2010) find that the mushroom body of the segmented worm Platynereis dumerilii shares many features with the mammalian cerebral cortex. The authors propose that the mushroom body and cortex evolved from the same structure in the common ancestor of vertebrates and invertebrates.","lang":"eng"}],"publication_status":"published"},{"quality_controlled":"1","citation":{"chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>.","apa":"Schanda, P., Meier, B. H., &#38; Ernst, M. (2010). Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>","mla":"Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45, American Chemical Society, 2010, pp. 15957–67, doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>.","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society 132 (2010) 15957–15967.","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45. American Chemical Society, pp. 15957–15967, 2010.","ama":"Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2010;132(45):15957-15967. doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>","ista":"Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the American Chemical Society. 132(45), 15957–15967."},"date_created":"2020-09-18T10:11:13Z","year":"2010","status":"public","day":"26","publication":"Journal of the American Chemical Society","doi":"10.1021/ja100726a","publication_identifier":{"issn":["0002-7863","1520-5126"]},"issue":"45","publication_status":"published","abstract":[{"lang":"eng","text":"Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins."}],"article_processing_charge":"No","page":"15957-15967","date_updated":"2021-01-12T08:19:30Z","publisher":"American Chemical Society","date_published":"2010-10-26T00:00:00Z","month":"10","language":[{"iso":"eng"}],"title":"Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy","volume":132,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"}],"oa_version":"None","intvolume":"       132","extern":"1","article_type":"original","_id":"8472"},{"abstract":[{"lang":"eng","text":"β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant."}],"publication_status":"published","page":"5827-5835","article_processing_charge":"No","publisher":"American Society for Biochemistry & Molecular Biology","date_updated":"2021-01-12T08:19:31Z","title":"Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR","language":[{"iso":"eng"}],"month":"02","keyword":["Cell Biology","Biochemistry","Molecular Biology"],"date_published":"2010-02-19T00:00:00Z","volume":285,"type":"journal_article","extern":"1","article_type":"original","author":[{"full_name":"Corazza, Alessandra","first_name":"Alessandra","last_name":"Corazza"},{"last_name":"Rennella","first_name":"Enrico","full_name":"Rennella, Enrico"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"first_name":"Maria Chiara","last_name":"Mimmi","full_name":"Mimmi, Maria Chiara"},{"full_name":"Cutuil, Thomas","last_name":"Cutuil","first_name":"Thomas"},{"full_name":"Raimondi, Sara","last_name":"Raimondi","first_name":"Sara"},{"first_name":"Sofia","last_name":"Giorgetti","full_name":"Giorgetti, Sofia"},{"full_name":"Fogolari, Federico","last_name":"Fogolari","first_name":"Federico"},{"full_name":"Viglino, Paolo","last_name":"Viglino","first_name":"Paolo"},{"full_name":"Frydman, Lucio","last_name":"Frydman","first_name":"Lucio"},{"full_name":"Gal, Maayan","first_name":"Maayan","last_name":"Gal"},{"full_name":"Bellotti, Vittorio","first_name":"Vittorio","last_name":"Bellotti"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"full_name":"Esposito, Gennaro","first_name":"Gennaro","last_name":"Esposito"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       285","oa_version":"None","_id":"8473","quality_controlled":"1","citation":{"ama":"Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. 2010;285(8):5827-5835. doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>","ista":"Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito G. 2010. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. Journal of Biological Chemistry. 285(8), 5827–5835.","short":"A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi, S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher, G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.","ieee":"A. Corazza <i>et al.</i>, “Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR,” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8. American Society for Biochemistry &#38; Molecular Biology, pp. 5827–5835, 2010.","mla":"Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8, American Society for Biochemistry &#38; Molecular Biology, 2010, pp. 5827–35, doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>.","apa":"Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi, S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>","chicago":"Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi, Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2010. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>."},"year":"2010","date_created":"2020-09-18T10:11:23Z","status":"public","day":"19","publication":"Journal of Biological Chemistry","issue":"8","doi":"10.1074/jbc.m109.061168","publication_identifier":{"issn":["0021-9258","1083-351X"]}},{"article_processing_charge":"No","page":"43-87","publication_status":"published","date_published":"2010-01-01T00:00:00Z","title":"Prevalence","month":"01","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:45Z","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Hunt, Brian R.","last_name":"Hunt","first_name":"Brian R."},{"first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"}],"intvolume":"         3","oa_version":"None","extern":"1","type":"book_chapter","volume":3,"_id":"8506","citation":{"mla":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87, doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>.","chicago":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In <i>Handbook of Dynamical Systems</i>, 3:43–87. Elsevier, 2010. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>.","apa":"Hunt, B. R., &#38; Kaloshin, V. (2010). Prevalence. In <i>Handbook of Dynamical Systems</i> (Vol. 3, pp. 43–87). Elsevier. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>","ista":"Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems. vol. 3, 43–87.","ama":"Hunt BR, Kaloshin V. Prevalence. In: <i>Handbook of Dynamical Systems</i>. Vol 3. Elsevier; 2010:43-87. doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>","ieee":"B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87.","short":"B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010, pp. 43–87."},"quality_controlled":"1","date_created":"2020-09-18T10:47:48Z","year":"2010","doi":"10.1016/s1874-575x(10)00310-3","publication_identifier":{"isbn":["9780444531414"],"issn":["1874-575X"]},"publication":"Handbook of Dynamical Systems","status":"public","day":"01"},{"type":"conference","extern":"1","author":[{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"full_name":"ZHANG, KE","last_name":"ZHANG","first_name":"KE"},{"full_name":"ZHENG, YONG","last_name":"ZHENG","first_name":"YONG"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8507","abstract":[{"lang":"eng","text":"We study a Cr nearly integrable Hamiltonian system  defined on 𝕋3 × ℝ3. Let  and µΣ1 be the restriction of Lebesgue measure on 𝕋3 × ℝ3 to ∑. We prove there is a perturbation ,  and an orbit (q(t), p(t)): ℝ → 𝕋3 × ℝ3 of the Hamiltonian equation  such that ."}],"publication_status":"published","page":"314-322","article_processing_charge":"No","publisher":"World Scientific","date_updated":"2021-01-12T08:19:46Z","language":[{"iso":"eng"}],"month":"03","title":"Almost dense orbit on energy surface","date_published":"2010-03-01T00:00:00Z","year":"2010","date_created":"2020-09-18T10:47:56Z","status":"public","day":"01","publication":"XVIth International Congress on Mathematical Physics","doi":"10.1142/9789814304634_0017","publication_identifier":{"isbn":["9789814304627","9789814304634"]},"quality_controlled":"1","citation":{"ama":"Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: <i>XVIth International Congress on Mathematical Physics</i>. World Scientific; 2010:314-322. doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>","ista":"Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface. XVIth International Congress on Mathematical Physics. International Congress on Mathematical Physics, 314–322.","short":"V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical Physics, World Scientific, 2010, pp. 314–322.","ieee":"V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,” in <i>XVIth International Congress on Mathematical Physics</i>, Prague, Czech Republic, 2010, pp. 314–322.","mla":"Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” <i>XVIth International Congress on Mathematical Physics</i>, World Scientific, 2010, pp. 314–22, doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>.","apa":"Kaloshin, V., ZHANG, K., &#38; ZHENG, Y. (2010). Almost dense orbit on energy surface. In <i>XVIth International Congress on Mathematical Physics</i> (pp. 314–322). Prague, Czech Republic: World Scientific. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>","chicago":"Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy Surface.” In <i>XVIth International Congress on Mathematical Physics</i>, 314–22. World Scientific, 2010. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>."},"conference":{"start_date":"2009-08-03","name":"International Congress on Mathematical Physics","location":"Prague, Czech Republic","end_date":"2009-08-08"}},{"volume":465,"acknowledgement":"We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.\n","type":"journal_article","extern":1,"intvolume":"       465","author":[{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"_id":"857","publist_id":"6791","abstract":[{"text":"The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.","lang":"eng"}],"publication_status":"published","page":"922 - 926","publisher":"Nature Publishing Group","date_updated":"2021-01-12T08:20:05Z","title":"Sequence space and the ongoing expansion of the protein universe","month":"06","date_published":"2010-06-17T00:00:00Z","year":"2010","date_created":"2018-12-11T11:48:52Z","day":"17","status":"public","publication":"Nature","issue":"7300","doi":"10.1038/nature09105","quality_controlled":0,"citation":{"mla":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>.","chicago":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>.","apa":"Povolotskaya, I., &#38; Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>","ista":"Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.","ama":"Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. 2010;465(7300):922-926. doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>","short":"I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.","ieee":"I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” <i>Nature</i>, vol. 465, no. 7300. Nature Publishing Group, pp. 922–926, 2010."}},{"abstract":[{"text":"A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.","lang":"eng"}],"publication_status":"published","page":"279 - 282","publisher":"Nature Publishing Group","date_updated":"2021-01-12T08:20:20Z","title":"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness","month":"03","date_published":"2010-03-11T00:00:00Z","volume":464,"acknowledgement":"We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov and M. Breen for thoughtful discussions and critical reading of the manuscript.","type":"journal_article","extern":1,"intvolume":"       464","author":[{"full_name":"Meer, Margarita V","first_name":"Margarita","last_name":"Meer"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"},{"full_name":"Artzy-Randrup, Yael","first_name":"Yael","last_name":"Artzy Randrup"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"_id":"862","publist_id":"6784","quality_controlled":0,"citation":{"chicago":"Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>.","apa":"Meer, M., Kondrashov, A., Artzy Randrup, Y., &#38; Kondrashov, F. (2010). Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>","mla":"Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>.","short":"M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.","ieee":"M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” <i>Nature</i>, vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.","ista":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.","ama":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. 2010;464(7286):279-282. doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>"},"year":"2010","date_created":"2018-12-11T11:48:54Z","day":"11","status":"public","publication":"Nature","issue":"7286","doi":"10.1038/nature08691"}]