[{"oa_version":"Preprint","date_published":"2010-08-20T00:00:00Z","publication_status":"published","doi":"10.1103/physrevlett.105.088304","intvolume":"       105","citation":{"ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation and effective temperature of active colloidal suspensions,” <i>Physical Review Letters</i>, vol. 105, no. 8. American Physical Society , 2010.","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. 2010;105(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 105 (2010).","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>","mla":"Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>, vol. 105, no. 8, 088304, American Physical Society , 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>.","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and effective temperature of active colloidal suspensions. Physical Review Letters. 105(8), 088304.","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>. American Physical Society , 2010. <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1004.4340","open_access":"1"}],"scopus_import":"1","article_number":"088304","_id":"9013","date_updated":"2023-02-23T13:46:42Z","abstract":[{"text":"In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.","lang":"eng"}],"arxiv":1,"issue":"8","year":"2010","month":"08","status":"public","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"oa":1,"type":"journal_article","language":[{"iso":"eng"}],"date_created":"2021-01-19T10:26:33Z","publication":"Physical Review Letters","external_id":{"arxiv":["1004.4340"],"pmid":["20868136"]},"quality_controlled":"1","volume":105,"article_processing_charge":"No","article_type":"letter_note","author":[{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A"},{"full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile","last_name":"Cottin-Bizonne"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"full_name":"Bocquet, Lydéric","first_name":"Lydéric","last_name":"Bocquet"}],"pmid":1,"day":"20","extern":"1","publisher":"American Physical Society ","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Sedimentation and effective temperature of active colloidal suspensions"},{"day":"09","extern":"1","author":[{"last_name":"O’Gorman","first_name":"P A","full_name":"O’Gorman, P A"},{"orcid":"0000-0001-5836-5350","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"}],"title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","publisher":"IOP Publishing","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-02-15T14:40:46Z","publication":"Environmental Research Letters","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"quality_controlled":"1","volume":5,"year":"2010","date_updated":"2022-01-24T13:51:02Z","abstract":[{"text":"The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.","lang":"eng"}],"issue":"2","_id":"9146","article_number":"025207","oa":1,"publication_identifier":{"issn":["1748-9326"]},"status":"public","month":"04","publication_status":"published","doi":"10.1088/1748-9326/5/2/025207","date_published":"2010-04-09T00:00:00Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1748-9326/5/2/025207"}],"citation":{"short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","ieee":"P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?,” <i>Environmental Research Letters</i>, vol. 5, no. 2. IOP Publishing, 2010.","ama":"O’Gorman PA, Muller CJ. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. 2010;5(2). doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>","chicago":"O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>. IOP Publishing, 2010. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>.","ista":"O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental Research Letters. 5(2), 025207.","apa":"O’Gorman, P. A., &#38; Muller, C. J. (2010). How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>","mla":"O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>, vol. 5, no. 2, 025207, IOP Publishing, 2010, doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>."},"intvolume":"         5"},{"publication_status":"published","doi":"10.1073/pnas.1009695107","oa_version":"Published Version","date_published":"2010-10-26T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1009695107"}],"scopus_import":"1","intvolume":"       107","citation":{"ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>."},"date_updated":"2021-12-14T08:40:02Z","issue":"43","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"year":"2010","_id":"9485","status":"public","oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"10","date_created":"2021-06-07T09:31:01Z","page":"18729-18734","publication":"Proceedings of the National Academy of Sciences","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"article_processing_charge":"No","article_type":"original","external_id":{"pmid":["20937895"]},"quality_controlled":"1","volume":107,"pmid":1,"day":"26","extern":"1","author":[{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"first_name":"Bradley","last_name":"Dotson","full_name":"Dotson, Bradley"},{"first_name":"Matthew D.","last_name":"Brooks","full_name":"Brooks, Matthew D."},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"publisher":"National Academy of Sciences","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Local DNA hypomethylation activates genes in rice endosperm"},{"extern":"1","day":"14","pmid":1,"author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier","publication":"Current Biology","page":"R780-R785","date_created":"2021-06-07T09:45:27Z","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"review","quality_controlled":"1","volume":20,"external_id":{"pmid":["20833323"]},"year":"2010","abstract":[{"lang":"eng","text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries."}],"issue":"17","date_updated":"2021-12-14T08:52:34Z","_id":"9489","oa":1,"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"status":"public","month":"09","doi":"10.1016/j.cub.2010.07.007","publication_status":"published","date_published":"2010-09-14T00:00:00Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"scopus_import":"1","intvolume":"        20","citation":{"ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785."}},{"language":[{"iso":"eng"}],"type":"journal_article","publication":"Soft Matter","page":"1874-1878","date_created":"2021-10-12T08:34:23Z","keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","volume":7,"external_id":{"arxiv":["1010.2453"]},"article_type":"original","article_processing_charge":"No","author":[{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"extern":"1","day":"23","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.","title":"Particle self-assembly on soft elastic shells","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Royal Society of Chemistry (RSC)","date_published":"2010-12-23T00:00:00Z","oa_version":"Preprint","doi":"10.1039/c0sm01143f","publication_status":"published","intvolume":"         7","citation":{"ista":"Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells. Soft Matter. 7(5), 1874–1878.","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>","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>.","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.","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>"},"main_file_link":[{"url":"https://arxiv.org/abs/1010.2453","open_access":"1"}],"_id":"10127","year":"2010","issue":"5","arxiv":1,"abstract":[{"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.","lang":"eng"}],"date_updated":"2021-10-12T09:49:27Z","month":"12","publication_identifier":{"issn":["1744-683X","1744-6848"]},"oa":1,"status":"public"},{"intvolume":"       115","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>.","ista":"Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 115(22), 7182–7189.","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>.","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."},"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1010.2458","open_access":"1"}],"oa_version":"Preprint","date_published":"2010-10-15T00:00:00Z","doi":"10.1021/jp107545w","publication_status":"published","month":"10","status":"public","oa":1,"publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"_id":"10390","issue":"22","arxiv":1,"abstract":[{"lang":"eng","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."}],"date_updated":"2021-11-29T16:20:29Z","year":"2010","volume":115,"quality_controlled":"1","keyword":["materials chemistry"],"external_id":{"arxiv":["1010.2458"],"pmid":["20949934"]},"article_processing_charge":"No","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication":"The Journal of Physical Chemistry B","date_created":"2021-11-29T15:13:17Z","page":"7182-7189","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Chemical Society","title":"Packing of soft asymmetric dumbbells","author":[{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Bozorgui","first_name":"Behnaz","full_name":"Bozorgui, Behnaz"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"pmid":1,"acknowledgement":"This work was supported by the National Science Foundation under CAREER Grant No. DMR-0846426 and partly by Columbia University.","extern":"1","day":"15"},{"language":[{"iso":"eng"}],"type":"journal_article","date_created":"2021-11-29T15:14:33Z","publication":"Physical Review Letters","external_id":{"arxiv":["1005.2429"],"pmid":["20867183"]},"keyword":["general physics and astronomy"],"volume":104,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","author":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Josep C.","last_name":"Pàmies","full_name":"Pàmies, Josep C."},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"day":"03","extern":"1","pmid":1,"acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.","title":"Effective elasticity of a flexible filament bound to a deformable cylindrical surface","publisher":"American Physical Society","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2010-06-03T00:00:00Z","oa_version":"Preprint","publication_status":"published","doi":"10.1103/physrevlett.104.226101","intvolume":"       104","citation":{"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>","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>.","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.","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>.","short":"A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010).","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.","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>"},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1005.2429"}],"_id":"10391","article_number":"226101","year":"2010","date_updated":"2021-11-30T08:11:19Z","abstract":[{"lang":"eng","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."}],"arxiv":1,"issue":"22","month":"06","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa":1,"status":"public"},{"article_processing_charge":"No","publist_id":"6345","volume":6,"external_id":{"arxiv":["0909.4700"]},"publication":"Nature Physics","date_created":"2018-12-11T11:49:51Z","page":"265 - 270","language":[{"iso":"eng"}],"type":"journal_article","title":"An ultracold high-density sample of rovibronic ground-state molecules in an optical lattice","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","extern":"1","day":"04","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.","author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"first_name":"Elmar","last_name":"Haller","full_name":"Haller, Elmar"},{"full_name":"Gustavsson, Mattias","last_name":"Gustavsson","first_name":"Mattias"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"first_name":"Jesus","last_name":"Aldegunde","full_name":"Aldegunde, Jesus"},{"last_name":"Hutson","first_name":"Jeremy","full_name":"Hutson, Jeremy"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0909.4700"}],"citation":{"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>.","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>.","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>","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.","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.","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>","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J. Aldegunde, J. Hutson, H. Nägerl, Nature Physics 6 (2010) 265–270."},"intvolume":"         6","doi":"10.1038/nphys1533","publication_status":"published","date_published":"2010-04-04T00:00:00Z","oa_version":"Preprint","oa":1,"status":"public","month":"04","year":"2010","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"}],"arxiv":1,"issue":"4","date_updated":"2021-01-12T06:47:53Z","_id":"1044"},{"main_file_link":[{"url":"https://arxiv.org/abs/1002.3795","open_access":"1"}],"intvolume":"       104","citation":{"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).","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>","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>.","short":"E. Haller, M. Mark, R. Hart, J.G. Danzl, L. Reichsöllner, V. Melezhik, P. Schmelcher, H. Nägerl, Physical Review Letters 104 (2010).","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.","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>"},"doi":"10.1103/PhysRevLett.104.153203","publication_status":"published","date_published":"2010-04-14T00:00:00Z","oa_version":"Preprint","oa":1,"status":"public","month":"04","year":"2010","issue":"15","arxiv":1,"abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T06:47:53Z","_id":"1045","article_processing_charge":"No","publist_id":"6344","volume":104,"external_id":{"arxiv":["1002.3795"]},"publication":"Physical Review Letters","date_created":"2018-12-11T11:49:51Z","language":[{"iso":"eng"}],"type":"journal_article","title":"Confinement-induced resonances in low-dimensional quantum systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","extern":"1","day":"14","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.","author":[{"full_name":"Haller, Elmar","first_name":"Elmar","last_name":"Haller"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"last_name":"Hart","first_name":"Russell","full_name":"Hart, Russell"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Reichsöllner","first_name":"Lukas","full_name":"Reichsöllner, Lukas"},{"full_name":"Melezhik, Vladimir","last_name":"Melezhik","first_name":"Vladimir"},{"full_name":"Schmelcher, Peter","last_name":"Schmelcher","first_name":"Peter"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}]},{"_id":"1047","year":"2010","date_updated":"2021-01-12T06:47:54Z","arxiv":1,"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."}],"issue":"20","month":"05","oa":1,"status":"public","date_published":"2010-05-21T00:00:00Z","oa_version":"Preprint","publication_status":"published","doi":"10.1103/PhysRevLett.104.200403","citation":{"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.","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>","short":"E. Haller, R. Hart, M. Mark, J.G. Danzl, L. Reichsöllner, H. Nägerl, Physical Review Letters 104 (2010).","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>","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).","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>.","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>."},"intvolume":"       104","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1001.1206"}],"author":[{"last_name":"Haller","first_name":"Elmar","full_name":"Haller, Elmar"},{"last_name":"Hart","first_name":"Russell","full_name":"Hart, Russell"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"full_name":"Reichsöllner, Lukas","last_name":"Reichsöllner","first_name":"Lukas"},{"first_name":"Hanns","last_name":"Nägerl","full_name":"Nägerl, Hanns"}],"day":"21","extern":"1","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.","title":"Inducing transport in a dissipation-free lattice with super bloch oscillations","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:49:52Z","publication":"Physical Review Letters","external_id":{"arxiv":["1001.1206"]},"volume":104,"publist_id":"6343","article_processing_charge":"No"},{"_id":"1049","date_updated":"2021-01-12T06:47:54Z","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."}],"arxiv":1,"issue":"7306","year":"2010","month":"07","status":"public","oa":1,"oa_version":"Preprint","date_published":"2010-07-29T00:00:00Z","publication_status":"published","doi":"10.1038/nature09259","citation":{"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.","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>","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.","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>.","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>","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>.","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."},"intvolume":"       466","main_file_link":[{"url":"https://arxiv.org/abs/1004.3168","open_access":"1"}],"author":[{"first_name":"Elmar","last_name":"Haller","full_name":"Haller, Elmar"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"full_name":"Mark, Manfred","last_name":"Mark","first_name":"Manfred"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Reichsöllner, Lukas","first_name":"Lukas","last_name":"Reichsöllner"},{"first_name":"Mattias","last_name":"Gustavsson","full_name":"Gustavsson, Mattias"},{"last_name":"Dalmonte","first_name":"Marcello","full_name":"Dalmonte, Marcello"},{"first_name":"Guido","last_name":"Pupillo","full_name":"Pupillo, Guido"},{"first_name":"Hanns","last_name":"Nägerl","full_name":"Nägerl, Hanns"}],"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.","day":"29","extern":"1","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Pinning quantum phase transition for a Luttinger liquid of strongly interacting bosons","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:52Z","page":"597 - 600","publication":"Nature","external_id":{"arxiv":["1004.3168"]},"volume":466,"publist_id":"6341","article_processing_charge":"No"},{"article_processing_charge":"No","quality_controlled":"1","volume":6346,"external_id":{"arxiv":["1001.5076"]},"publication":"18th Annual European Symposium on Algorithms","page":"182–194","date_created":"2022-08-11T12:14:20Z","type":"conference","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"Online stochastic packing applied to display ad allocation","alternative_title":["LNCS"],"extern":"1","day":"01","author":[{"last_name":"Feldman","first_name":"Jon","full_name":"Feldman, Jon"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"first_name":"Nitish","last_name":"Korula","full_name":"Korula, Nitish"},{"first_name":"Vahab S.","last_name":"Mirrokni","full_name":"Mirrokni, Vahab S."},{"last_name":"Stein","first_name":"Cliff","full_name":"Stein, Cliff"}],"main_file_link":[{"url":"https://arxiv.org/abs/1001.5076","open_access":"1"}],"scopus_import":"1","citation":{"apa":"Feldman, J., Henzinger, M. H., Korula, N., Mirrokni, V. S., &#38; Stein, C. (2010). Online stochastic packing applied to display ad allocation. In <i>18th Annual European Symposium on Algorithms</i> (Vol. 6346, pp. 182–194). Liverpool, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-15775-2_16\">https://doi.org/10.1007/978-3-642-15775-2_16</a>","ista":"Feldman J, Henzinger MH, Korula N, Mirrokni VS, Stein C. 2010. Online stochastic packing applied to display ad allocation. 18th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 6346, 182–194.","mla":"Feldman, Jon, et al. “Online Stochastic Packing Applied to Display Ad Allocation.” <i>18th Annual European Symposium on Algorithms</i>, vol. 6346, Springer Nature, 2010, pp. 182–194, doi:<a href=\"https://doi.org/10.1007/978-3-642-15775-2_16\">10.1007/978-3-642-15775-2_16</a>.","chicago":"Feldman, Jon, Monika H Henzinger, Nitish Korula, Vahab S. Mirrokni, and Cliff Stein. “Online Stochastic Packing Applied to Display Ad Allocation.” In <i>18th Annual European Symposium on Algorithms</i>, 6346:182–194. Springer Nature, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15775-2_16\">https://doi.org/10.1007/978-3-642-15775-2_16</a>.","short":"J. Feldman, M.H. Henzinger, N. Korula, V.S. Mirrokni, C. Stein, in:, 18th Annual European Symposium on Algorithms, Springer Nature, 2010, pp. 182–194.","ieee":"J. Feldman, M. H. Henzinger, N. Korula, V. S. Mirrokni, and C. Stein, “Online stochastic packing applied to display ad allocation,” in <i>18th Annual European Symposium on Algorithms</i>, Liverpool, United Kingdom, 2010, vol. 6346, pp. 182–194.","ama":"Feldman J, Henzinger MH, Korula N, Mirrokni VS, Stein C. Online stochastic packing applied to display ad allocation. In: <i>18th Annual European Symposium on Algorithms</i>. Vol 6346. Springer Nature; 2010:182–194. doi:<a href=\"https://doi.org/10.1007/978-3-642-15775-2_16\">10.1007/978-3-642-15775-2_16</a>"},"intvolume":"      6346","doi":"10.1007/978-3-642-15775-2_16","conference":{"location":"Liverpool, United Kingdom","end_date":"2010-09-08","name":"ESA: European Symposium on Algorithms","start_date":"2010-09-06"},"publication_status":"published","oa_version":"Preprint","date_published":"2010-09-01T00:00:00Z","status":"public","publication_identifier":{"isbn":["3642157742"],"issn":["1611-3349"]},"oa":1,"month":"09","arxiv":1,"abstract":[{"text":"Inspired by online ad allocation, we study online stochastic packing integer programs from theoretical and practical standpoints. We first present a near-optimal online algorithm for a general class of packing integer programs which model various online resource allocation problems including online variants of routing, ad allocations, generalized assignment, and combinatorial auctions. As our main theoretical result, we prove that a simple dual training-based algorithm achieves a (1 − o(1))-approximation guarantee in the random order stochastic model. This is a significant improvement over logarithmic or constant-factor approximations for the adversarial variants of the same problems (e.g. factor 1−1𝑒 for online ad allocation, and log(m) for online routing). We then focus on the online display ad allocation problem and study the efficiency and fairness of various training-based and online allocation algorithms on data sets collected from real-life display ad allocation system. Our experimental evaluation confirms the effectiveness of training-based algorithms on real data sets, and also indicates an intrinsic trade-off between fairness and efficiency.","lang":"eng"}],"date_updated":"2023-02-13T11:36:46Z","year":"2010","_id":"11797"},{"intvolume":"         5","citation":{"ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria, and the Hungarian Method,” in <i>27th International Symposium on Theoretical Aspects of Computer Science</i>, Nancy, France, 2010, vol. 5, pp. 287–298.","ama":"Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and the Hungarian Method. In: <i>27th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 5. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:287-298. doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2010.2463\">10.4230/LIPICS.STACS.2010.2463</a>","short":"P. Dütting, M.H. Henzinger, I. Weber, in:, 27th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 287–298.","apa":"Dütting, P., Henzinger, M. H., &#38; Weber, I. (2010). Sponsored search, market equilibria, and the Hungarian Method. In <i>27th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 5, pp. 287–298). Nancy, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2010.2463\">https://doi.org/10.4230/LIPICS.STACS.2010.2463</a>","ista":"Dütting P, Henzinger MH, Weber I. 2010. Sponsored search, market equilibria, and the Hungarian Method. 27th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 5, 287–298.","mla":"Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian Method.” <i>27th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 287–98, doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2010.2463\">10.4230/LIPICS.STACS.2010.2463</a>.","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search, Market Equilibria, and the Hungarian Method.” In <i>27th International Symposium on Theoretical Aspects of Computer Science</i>, 5:287–98. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2010.2463\">https://doi.org/10.4230/LIPICS.STACS.2010.2463</a>."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.STACS.2010.2463"}],"date_published":"2010-03-09T00:00:00Z","oa_version":"Published Version","doi":"10.4230/LIPICS.STACS.2010.2463","conference":{"end_date":"2010-03-06","location":"Nancy, France","start_date":"2010-03-04","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"publication_status":"published","month":"03","oa":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-939897-16-3"]},"status":"public","_id":"11838","year":"2010","arxiv":1,"abstract":[{"text":"Two-sided matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market where $n$ advertisers compete for the assignment of one of $k$ sponsored search results, also known as ``slots'', for certain keywords they are interested in. Here, as in other markets of that kind, market equilibria correspond to stable matchings. In this paper, we show how to modify Kuhn's Hungarian Method (Kuhn, 1955) so that it finds an optimal stable matching between advertisers and advertising slots in settings with generalized linear utilities, per-bidder-item reserve prices, and per-bidder-item maximum prices. The only algorithm for this problem presented so far (Aggarwal et al., 2009) requires the market to be in ''general position''. We do not make this assumption.","lang":"eng"}],"date_updated":"2023-02-21T16:30:02Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"11838"}]},"volume":5,"quality_controlled":"1","external_id":{"arxiv":["0912.1934"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"conference","publication":"27th International Symposium on Theoretical Aspects of Computer Science","date_created":"2022-08-12T11:45:49Z","page":"287-298","alternative_title":["LIPIcs"],"title":"Sponsored search, market equilibria, and the Hungarian Method","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Dütting, Paul","first_name":"Paul","last_name":"Dütting"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Weber, Ingmar","last_name":"Weber","first_name":"Ingmar"}],"extern":"1","day":"09"},{"keyword":["Water Science and Technology"],"quality_controlled":"1","volume":46,"article_processing_charge":"No","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication":"Water Resources Research","date_created":"2023-02-20T08:18:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Geophysical Union","title":"Effect of glaciers on streamflow trends in the Swiss Alps","author":[{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"},{"full_name":"Bauder, A.","first_name":"A.","last_name":"Bauder"},{"full_name":"Parola, M.","last_name":"Parola","first_name":"M."}],"extern":"1","day":"01","citation":{"chicago":"Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>. American Geophysical Union, 2010. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>.","apa":"Pellicciotti, F., Bauder, A., &#38; Parola, M. (2010). Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>","mla":"Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>, vol. 46, no. 10, W10522, American Geophysical Union, 2010, doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>.","ista":"Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow trends in the Swiss Alps. Water Resources Research. 46(10), W10522.","ieee":"F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow trends in the Swiss Alps,” <i>Water Resources Research</i>, vol. 46, no. 10. American Geophysical Union, 2010.","ama":"Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. 2010;46(10). doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>","short":"F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010)."},"intvolume":"        46","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2009WR009039"}],"oa_version":"Published Version","date_published":"2010-10-01T00:00:00Z","doi":"10.1029/2009wr009039","publication_status":"published","month":"10","status":"public","oa":1,"publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"article_number":"W10522","_id":"12653","abstract":[{"text":"Daily streamflow from stations close to five Swiss glaciers is analyzed for trends with the Mann-Kendall test. We consider a common period of record (1974–2004) and longer periods based on data availability. The trend statistical significance is tested on annual and seasonal bases. We also examine changes in precipitation, temperature, and snow cover characteristics. Highly glacierized basins show statistically significant positive trends in annual streamflow caused by increasing streamflow in spring and summer. Trends are more numerous and stronger at lower and mid than at the upper quantiles. The basin characterized by lower glacier coverage, conversely, does not exhibit consistently statistically significant trends. Changes in precipitation are not sufficient to explain the observed streamflow trends. Air temperature sees an increase in mean, minimum, and maximum values at all sites. Variations in the seasonal snow accumulation and ablation process are evident. Solid precipitation is decreasing at all sites and trends may be due to a shift from snowfall into rainfall. Mean snow depth is also decreasing, and its duration is getting shorter because of a decrease in solid precipitation and enhanced melting. Trend magnitude attenuates with longer time series. Contrasting trends are detected for different subperiods in the last 70 years: statistically significant negative trends are observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast with the results for the common period. These trends are explained by different rates of ice volume changes, and the sign of trends is clearly related to phases of positive or negative glacier mass balance.","lang":"eng"}],"issue":"10","date_updated":"2023-02-20T09:39:29Z","year":"2010"},{"month":"06","status":"public","publisher":"Elsevier","oa":1,"title":"Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics","author":[{"full_name":"Gasper Tkacik","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"_id":"3430","abstract":[{"text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.","lang":"eng"}],"date_updated":"2021-01-12T07:43:25Z","year":"2010","extern":1,"day":"22","quality_controlled":0,"citation":{"chicago":"Tkačik, Gašper. “Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics.” Elsevier, 2010.","mla":"Tkačik, Gašper. <i>Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics</i>. Elsevier, 2010.","apa":"Tkačik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, Elsevier.","ista":"Tkačik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative Genomics.","ieee":"G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.","ama":"Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.","short":"G. Tkačik, in:, Elsevier, 2010."},"publist_id":"2970","main_file_link":[{"url":"http://arxiv.org/pdf/1006.4291","open_access":"1"}],"type":"conference","date_published":"2010-06-22T00:00:00Z","publication_status":"published","conference":{"name":"Summer School on Quantitative Evolutionary and Comparative Genomics"},"date_created":"2018-12-11T12:03:17Z"},{"volume":30,"intvolume":"        30","quality_controlled":"1","citation":{"ieee":"P. Jiruska <i>et al.</i>, “High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro,” <i>Journal of Neuroscience</i>, vol. 30, no. 16. Society for Neuroscience, pp. 5690–5701, 2010.","ama":"Jiruska P, Csicsvari JL, Powell A, et al. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. <i>Journal of Neuroscience</i>. 2010;30(16):5690-5701. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">10.1523/JNEUROSCI.0535-10.2010</a>","short":"P. Jiruska, J.L. Csicsvari, A. Powell, J. Fox, W. Chang, M. Vreugdenhil, X. Li, M. Palus, A. Bujan, R. Dearden, J. Jefferys, Journal of Neuroscience 30 (2010) 5690–5701.","chicago":"Jiruska, Premysl, Jozsef L Csicsvari, Andrew Powell, John Fox, Wei Chang, Martin Vreugdenhil, Xiaoli Li, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2010. <a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">https://doi.org/10.1523/JNEUROSCI.0535-10.2010</a>.","ista":"Jiruska P, Csicsvari JL, Powell A, Fox J, Chang W, Vreugdenhil M, Li X, Palus M, Bujan A, Dearden R, Jefferys J. 2010. High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. Journal of Neuroscience. 30(16), 5690–5701.","apa":"Jiruska, P., Csicsvari, J. L., Powell, A., Fox, J., Chang, W., Vreugdenhil, M., … Jefferys, J. (2010). High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">https://doi.org/10.1523/JNEUROSCI.0535-10.2010</a>","mla":"Jiruska, Premysl, et al. “High-Frequency Network Activity, Global Increase in Neuronal Activity, and Synchrony Expansion Precede Epileptic Seizures in Vitro.” <i>Journal of Neuroscience</i>, vol. 30, no. 16, Society for Neuroscience, 2010, pp. 5690–701, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0535-10.2010\">10.1523/JNEUROSCI.0535-10.2010</a>."},"main_file_link":[{"url":"http://www.jneurosci.org/content/30/16/5690","open_access":"1"}],"publist_id":"2848","oa_version":"None","type":"journal_article","date_published":"2010-04-21T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0535-10.2010","publication_status":"published","publication":"Journal of Neuroscience","date_created":"2018-12-11T12:03:51Z","page":"5690 - 5701","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Neuroscience","status":"public","oa":1,"title":"High-frequency network activity, global increase in neuronal activity, and synchrony expansion precede epileptic seizures in vitro","author":[{"full_name":"Jiruska, Premysl","first_name":"Premysl","last_name":"Jiruska"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"},{"full_name":"Powell, Andrew","first_name":"Andrew","last_name":"Powell"},{"full_name":"Fox, John","last_name":"Fox","first_name":"John"},{"full_name":"Chang, Wei","first_name":"Wei","last_name":"Chang"},{"full_name":"Vreugdenhil, Martin","first_name":"Martin","last_name":"Vreugdenhil"},{"last_name":"Li","first_name":"Xiaoli","full_name":"Li, Xiaoli"},{"first_name":"Milan","last_name":"Palus","full_name":"Palus, Milan"},{"last_name":"Bujan","first_name":"Alejandro","full_name":"Bujan, Alejandro"},{"first_name":"Richard","last_name":"Dearden","full_name":"Dearden, Richard"},{"last_name":"Jefferys","first_name":"John","full_name":"Jefferys, John"}],"_id":"3538","issue":"16","abstract":[{"text":"How seizures start is a major question in epilepsy research. Preictal EEG changes occur in both human patients and animal models, but their underlying mechanisms and relationship with seizure initiation remain unknown. Here we demonstrate the existence, in the hippocampal CA1 region, of a preictal state characterized by the progressive and global increase in neuronal activity associated with a widespread buildup of low-amplitude high-frequency activity (HFA) (&gt; 100 Hz) and reduction in system complexity. HFA is generated by the firing of neurons, mainly pyramidal cells, at much lower frequencies. Individual cycles of HFA are generated by the near-synchronous (within similar to 5 ms) firing of small numbers of pyramidal cells. The presence of HFA in the low-calcium model implicates nonsynaptic synchronization; the presence of very similar HFA in the high-potassium model shows that it does not depend on an absence of synaptic transmission. Immediately before seizure onset, CA1 is in a state of high sensitivity in which weak depolarizing or synchronizing perturbations can trigger seizures. Transition to seizure is characterized by a rapid expansion and fusion of the neuronal populations responsible for HFA, associated with a progressive slowing of HFA, leading to a single, massive, hypersynchronous cluster generating the high-amplitude low-frequency activity of the seizure.","lang":"eng"}],"date_updated":"2021-01-12T07:44:10Z","extern":"1","year":"2010","day":"21"},{"publisher":"Open Publishing Association","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Lumpability abstractions of rule-based systems","alternative_title":["EPTCS"],"acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","day":"30","author":[{"full_name":"Feret, Jérôme","last_name":"Feret","first_name":"Jérôme"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":907155,"checksum":"eaaba991a86fff37606b0eb5196878e8","creator":"kschuh","file_id":"5904","access_level":"open_access","date_updated":"2020-07-14T12:46:14Z","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","date_created":"2019-01-31T12:09:09Z"}],"publist_id":"2511","external_id":{"arxiv":["1011.0496"]},"volume":40,"quality_controlled":"1","related_material":{"record":[{"id":"3168","status":"public","relation":"later_version"}]},"has_accepted_license":"1","page":"142-161","date_created":"2018-12-11T12:04:47Z","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"status":"public","oa":1,"month":"10","date_updated":"2023-02-23T11:15:19Z","abstract":[{"text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.","lang":"eng"}],"arxiv":1,"year":"2010","_id":"3719","file_date_updated":"2020-07-14T12:46:14Z","scopus_import":1,"ddc":["570"],"citation":{"ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","mla":"Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association."},"intvolume":"        40","publication_status":"published","conference":{"location":"Jena, Germany","end_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","start_date":"2010-08-23"},"oa_version":"Submitted Version","date_published":"2010-10-30T00:00:00Z"},{"author":[{"full_name":"Gasper Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper"}],"_id":"3743","abstract":[{"text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes.","lang":"eng"}],"date_updated":"2021-01-12T07:51:53Z","year":"2010","extern":1,"day":"22","month":"06","publisher":"ArXiv","status":"public","oa":1,"title":"From statistical mechanics to information theory: understanding biophysical information-processing systems","type":"preprint","date_published":"2010-06-22T00:00:00Z","publication_status":"published","publication":"ArXiv","date_created":"2018-12-11T12:04:55Z","page":"1 - 52","volume":"q-bio.MN","quality_controlled":0,"citation":{"chicago":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>. ArXiv, 2010.","apa":"Tkačik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. ArXiv.","ista":"Tkačik G. 2010. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv, q-MN, 1–52, .","mla":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>, vol. q-MN, ArXiv, 2010, pp. 1–52.","ieee":"G. Tkačik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” <i>ArXiv</i>, vol. q-MN. ArXiv, pp. 1–52, 2010.","ama":"Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. 2010;q-MN:1-52.","short":"G. Tkačik, ArXiv q-MN (2010) 1–52."},"publist_id":"2487","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.4291v1"}]},{"volume":468,"citation":{"ama":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. 2010;468:819-823. doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>","ieee":"H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence of behavioural variability and response to small stimuli in bacteria,” <i>Nature</i>, vol. 468. Nature Publishing Group, pp. 819–823, 2010.","short":"H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468 (2010) 819–823.","chicago":"Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet, and Philippe Cluzel. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>.","apa":"Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., &#38; Cluzel, P. (2010). Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>","mla":"Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>, vol. 468, Nature Publishing Group, 2010, pp. 819–23, doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>.","ista":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 468, 819–823."},"intvolume":"       468","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230254"}],"publist_id":"2480","type":"journal_article","date_published":"2010-12-09T00:00:00Z","publication_status":"published","doi":"10.1038/nature09551","date_created":"2018-12-11T12:04:57Z","page":"819 - 823","publication":"Nature","month":"12","status":"public","publisher":"Nature Publishing Group","title":"Interdependence of behavioural variability and response to small stimuli in bacteria","oa":1,"author":[{"last_name":"Park","first_name":"Heungwon","full_name":"Park, Heungwon"},{"full_name":"Pontius, William","first_name":"William","last_name":"Pontius"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Calin Guet"},{"first_name":"John","last_name":"Marko","full_name":"Marko, John F"},{"last_name":"Emonet","first_name":"Thierry","full_name":"Emonet,Thierry"},{"full_name":"Cluzel,Philippe","first_name":"Philippe","last_name":"Cluzel"}],"_id":"3748","date_updated":"2021-01-12T07:51:55Z","abstract":[{"text":"The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence","lang":"eng"}],"day":"09","year":"2010","extern":1},{"author":[{"full_name":"Park, Heungwon","last_name":"Park","first_name":"Heungwon"},{"full_name":"Calin Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Emonet","first_name":"Thierry","full_name":"Emonet,Thierry"},{"last_name":"Cluzel","first_name":"Philippe","full_name":"Cluzel,Philippe"}],"_id":"3749","date_updated":"2021-01-12T07:51:55Z","issue":"3","abstract":[{"lang":"eng","text":"In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio."}],"acknowledgement":"P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID: PMC3230253 ","day":"23","year":"2010","extern":1,"month":"10","publisher":"Springer","status":"public","title":"Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay","oa":1,"type":"journal_article","date_published":"2010-10-23T00:00:00Z","publication_status":"published","doi":"10.1007/s00284-010-9778-z","date_created":"2018-12-11T12:04:57Z","page":"764 - 769","publication":"Current Microbiology","citation":{"chicago":"Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>.","apa":"Park, H., Guet, C. C., Emonet, T., &#38; Cluzel, P. (2010). Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. Springer. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>","ista":"Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. 62(3), 764–769.","mla":"Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>, vol. 62, no. 3, Springer, 2010, pp. 764–69, doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>.","ama":"Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. 2010;62(3):764-769. doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>","ieee":"H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay,” <i>Current Microbiology</i>, vol. 62, no. 3. Springer, pp. 764–769, 2010.","short":"H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010) 764–769."},"volume":62,"intvolume":"        62","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230253"}],"publist_id":"2479"}]