[{"abstract":[{"lang":"eng","text":"We prove a generating function formula for the Betti numbers of Nakajima quiver varieties. We prove that it is a q-deformation of the Weyl-Kac character formula. In particular this implies that the constant term of the polynomial counting the number of absolutely indecomposable representations of a quiver equals the multiplicity of a certain weight in the corresponding Kac-Moody algebra, which was conjectured by Kac in 1982."}],"day":"01","issue":"1","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel","first_name":"Tamas"}],"month":"07","extern":1,"date_published":"2010-07-01T00:00:00Z","quality_controlled":0,"status":"public","volume":181,"type":"journal_article","_id":"1465","date_updated":"2021-01-12T06:50:56Z","publication_status":"published","oa":1,"year":"2010","acknowledgement":"This work has been supported by a Royal Society University Research Fellowship, NSF grants DMS-0305505 and DMS-0604775 and an Alfred Sloan Fellowship 2005-2007.","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0811.1569"}],"publisher":"Springer","date_created":"2018-12-11T11:52:11Z","publication":"Inventiones Mathematicae","page":"21 - 37","citation":{"mla":"Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” <i>Inventiones Mathematicae</i>, vol. 181, no. 1, Springer, 2010, pp. 21–37, doi:<a href=\"https://doi.org/10.1007/s00222-010-0241-3\">10.1007/s00222-010-0241-3</a>.","chicago":"Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” <i>Inventiones Mathematicae</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00222-010-0241-3\">https://doi.org/10.1007/s00222-010-0241-3</a>.","ama":"Hausel T. Kac’s conjecture from Nakajima quiver varieties. <i>Inventiones Mathematicae</i>. 2010;181(1):21-37. doi:<a href=\"https://doi.org/10.1007/s00222-010-0241-3\">10.1007/s00222-010-0241-3</a>","ista":"Hausel T. 2010. Kac’s conjecture from Nakajima quiver varieties. Inventiones Mathematicae. 181(1), 21–37.","short":"T. Hausel, Inventiones Mathematicae 181 (2010) 21–37.","apa":"Hausel, T. (2010). Kac’s conjecture from Nakajima quiver varieties. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-010-0241-3\">https://doi.org/10.1007/s00222-010-0241-3</a>","ieee":"T. Hausel, “Kac’s conjecture from Nakajima quiver varieties,” <i>Inventiones Mathematicae</i>, vol. 181, no. 1. Springer, pp. 21–37, 2010."},"publist_id":"5730","title":"Kac's conjecture from Nakajima quiver varieties","intvolume":"       181","doi":"10.1007/s00222-010-0241-3"},{"citation":{"mla":"Hausel, Tamás, et al. “Topology of Character Varieties and Representations of Quivers.” <i>Comptes Rendus Mathematique</i>, vol. 348, no. 3–4, Elsevier, 2010, pp. 131–35, doi:<a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">10.1016/j.crma.2010.01.025</a>.","ama":"Hausel T, Letellier E, Rodríguez Villegas F. Topology of character varieties and representations of quivers. <i>Comptes Rendus Mathematique</i>. 2010;348(3-4):131-135. doi:<a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">10.1016/j.crma.2010.01.025</a>","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Topology of Character Varieties and Representations of Quivers.” <i>Comptes Rendus Mathematique</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">https://doi.org/10.1016/j.crma.2010.01.025</a>.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2010. Topology of character varieties and representations of quivers. Comptes Rendus Mathematique. 348(3–4), 131–135.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Comptes Rendus Mathematique 348 (2010) 131–135.","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2010). Topology of character varieties and representations of quivers. <i>Comptes Rendus Mathematique</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">https://doi.org/10.1016/j.crma.2010.01.025</a>","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Topology of character varieties and representations of quivers,” <i>Comptes Rendus Mathematique</i>, vol. 348, no. 3–4. Elsevier, pp. 131–135, 2010."},"page":"131 - 135","date_created":"2018-12-11T11:52:11Z","publication":"Comptes Rendus Mathematique","publisher":"Elsevier","intvolume":"       348","doi":"10.1016/j.crma.2010.01.025","publist_id":"5731","title":"Topology of character varieties and representations of quivers","year":"2010","publication_status":"published","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/0905.3491","open_access":"1"}],"status":"public","quality_controlled":0,"_id":"1466","type":"journal_article","date_updated":"2021-01-12T06:50:56Z","volume":348,"issue":"3-4","day":"01","abstract":[{"lang":"eng","text":"In Hausel et al. (2008) [10] we presented a conjecture generalizing the Cauchy formula for Macdonald polynomial. This conjecture encodes the mixed Hodge polynomials of the character varieties of representations of the fundamental group of a punctured Riemann surface of genus g. We proved several results which support this conjecture. Here we announce new results which are consequences of those in Hausel et al. (2008) [10]."}],"extern":1,"date_published":"2010-02-01T00:00:00Z","month":"02","author":[{"first_name":"Tamas","full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"last_name":"Letellier","first_name":"Emmanuel","full_name":"Letellier, Emmanuel"},{"last_name":"Rodríguez Villegas","first_name":"Fernando","full_name":"Rodríguez Villegas, Fernando"}]},{"month":"09","date_published":"2010-09-01T00:00:00Z","extern":1,"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas","full_name":"Tamas Hausel"}],"day":"01","abstract":[{"text":"This chapter surveys the motivations, related results, and progress made towards the following problem, raised by Hitchin in 1995: What is the space of L2 harmonic forms on the moduli space of Higgs bundles on a Riemann surface?","lang":"eng"}],"type":"book_chapter","_id":"1468","date_updated":"2021-01-12T06:50:57Z","status":"public","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/0709.0504","open_access":"1"}],"year":"2010","publication_status":"published","oa":1,"doi":"10.1093/acprof:oso/9780199534920.003.0016","publist_id":"5729","title":"S-Duality in HyperkäHler Hodge Theory","citation":{"apa":"Hausel, T. (2010). S-Duality in HyperkäHler Hodge Theory. In <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">https://doi.org/10.1093/acprof:oso/9780199534920.003.0016</a>","ieee":"T. Hausel, “S-Duality in HyperkäHler Hodge Theory,” in <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>, Oxford University Press, 2010.","mla":"Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>, Oxford University Press, 2010, doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">10.1093/acprof:oso/9780199534920.003.0016</a>.","ama":"Hausel T. S-Duality in HyperkäHler Hodge Theory. In: <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press; 2010. doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">10.1093/acprof:oso/9780199534920.003.0016</a>","chicago":"Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” In <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">https://doi.org/10.1093/acprof:oso/9780199534920.003.0016</a>.","ista":"Hausel T. 2010.S-Duality in HyperkäHler Hodge Theory. In: The Many Facets of Geometry: A Tribute to Nigel Hitchin. .","short":"T. Hausel, in:, The Many Facets of Geometry: A Tribute to Nigel Hitchin, Oxford University Press, 2010."},"publisher":"Oxford University Press","date_created":"2018-12-11T11:52:12Z","publication":"The Many Facets of Geometry: A Tribute to Nigel Hitchin"},{"title":"Adaptive Methods in BCI Research - An Introductory Tutorial","doi":"10.1007/978-3-642-02091-9_18","publication":"Brain-Computer Interfaces","date_created":"2024-02-14T09:56:00Z","editor":[{"first_name":"Bernhard","full_name":"Graimann, Bernhard","last_name":"Graimann"},{"first_name":"Gert","full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller"},{"last_name":"Allison","first_name":"Brendan","full_name":"Allison, Brendan"}],"page":"331-355","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5 Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore, we thank Matthias Krauledat for fruitful discussions and tools for generating Fig. 5.","edition":"1","type":"book_chapter","_id":"14983","date_updated":"2024-02-19T09:47:25Z","quality_controlled":"1","status":"public","author":[{"first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"last_name":"Vidaurre","first_name":"Carmen","full_name":"Vidaurre, Carmen"},{"first_name":"Klaus-Robert","full_name":"Müller, Klaus-Robert","last_name":"Müller"}],"date_published":"2010-09-06T00:00:00Z","language":[{"iso":"eng"}],"place":"Berlin, Heidelberg","publication_identifier":{"isbn":["9783642020902"],"eisbn":["9783642020919"],"issn":["1612-3018"]},"publisher":"Springer","citation":{"ama":"Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. <i>Brain-Computer Interfaces</i>. 1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>","chicago":"Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods in BCI Research - An Introductory Tutorial.” In <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed., 331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>.","mla":"Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory Tutorial.” <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann et al., 1st ed., Springer, 2010, pp. 331–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>.","short":"A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller, B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg, 2010, pp. 331–355.","ista":"Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research - An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection, , 331–355.","ieee":"A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in <i>Brain-Computer Interfaces</i>, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355.","apa":"Schlögl, A., Vidaurre, C., &#38; Müller, K.-R. (2010). Adaptive Methods in BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &#38; B. Allison (Eds.), <i>Brain-Computer Interfaces</i> (1st ed., pp. 331–355). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>"},"alternative_title":["The Frontiers Collection"],"publication_status":"published","year":"2010","series_title":"FRONTCOLL","month":"09","department":[{"_id":"ScienComp"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data."}],"oa_version":"None","day":"06"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Immobilized azobenzenes for the construction of photoresponsive materials","doi":"10.1351/pac-con-10-09-04","publication":"Pure and Applied Chemistry","date_created":"2023-08-01T09:48:11Z","page":"2247-2279","author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal"}],"scopus_import":"1","date_published":"2010-10-15T00:00:00Z","extern":"1","language":[{"iso":"eng"}],"volume":82,"type":"journal_article","_id":"13409","date_updated":"2023-08-08T07:58:13Z","keyword":["General Chemical Engineering","General Chemistry"],"quality_controlled":"1","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1351/pac-con-10-09-04"}],"oa":1,"publication_status":"published","year":"2010","publication_identifier":{"eissn":["1365-3075"],"issn":["0033-4545"]},"intvolume":"        82","publisher":"De Gruyter","citation":{"short":"R. Klajn, Pure and Applied Chemistry 82 (2010) 2247–2279.","ista":"Klajn R. 2010. Immobilized azobenzenes for the construction of photoresponsive materials. Pure and Applied Chemistry. 82(12), 2247–2279.","ama":"Klajn R. Immobilized azobenzenes for the construction of photoresponsive materials. <i>Pure and Applied Chemistry</i>. 2010;82(12):2247-2279. doi:<a href=\"https://doi.org/10.1351/pac-con-10-09-04\">10.1351/pac-con-10-09-04</a>","chicago":"Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive Materials.” <i>Pure and Applied Chemistry</i>. De Gruyter, 2010. <a href=\"https://doi.org/10.1351/pac-con-10-09-04\">https://doi.org/10.1351/pac-con-10-09-04</a>.","mla":"Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive Materials.” <i>Pure and Applied Chemistry</i>, vol. 82, no. 12, De Gruyter, 2010, pp. 2247–79, doi:<a href=\"https://doi.org/10.1351/pac-con-10-09-04\">10.1351/pac-con-10-09-04</a>.","ieee":"R. Klajn, “Immobilized azobenzenes for the construction of photoresponsive materials,” <i>Pure and Applied Chemistry</i>, vol. 82, no. 12. De Gruyter, pp. 2247–2279, 2010.","apa":"Klajn, R. (2010). Immobilized azobenzenes for the construction of photoresponsive materials. <i>Pure and Applied Chemistry</i>. De Gruyter. <a href=\"https://doi.org/10.1351/pac-con-10-09-04\">https://doi.org/10.1351/pac-con-10-09-04</a>"},"article_processing_charge":"No","month":"10","abstract":[{"text":"The immobilization of molecular switches onto inorganic supports has recently become a hot topic as it can give rise to novel hybrid materials in which the properties of the two components are mutually enhanced. Even more attractive is the concept of “transferring” the switchable characteristics of single layers of organic molecules onto the underlying inorganic components, rendering them responsive to external stimuli as well. Of the various molecular switches studied, azobenzene (AB) has arguably attracted most attention due to its simple molecular structure, and because its “trigger” (light) is a noninvasive one, it can be delivered instantaneously, and into a precise location. In order to fully realize its potential, however, it is necessary to immobilize AB onto solid supports. It is the goal of this manuscript to comprehensively yet concisely review such hybrid systems which comprise AB forming well-defined self-assembled monolayers (SAMs) on planar and curved (colloidal and nanoporous) inorganic surfaces. I discuss methods to immobilize AB derivatives onto surfaces, strategies to ensure efficient AB isomerization, ways to monitor the switching process, properties of these switchable hybrid materials, and, last but not least, their emerging applications.","lang":"eng"}],"article_type":"original","issue":"12","day":"15","oa_version":"Published Version"},{"year":"2010","publication_status":"published","citation":{"ista":"Coskun A, Wesson PJ, Klajn R, Trabolsi A, Fang L, Olson MA, Dey SK, Grzybowski BA, Stoddart JF. 2010. Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. Journal of the American Chemical Society. 132(12), 4310–4320.","short":"A. Coskun, P.J. Wesson, R. Klajn, A. Trabolsi, L. Fang, M.A. Olson, S.K. Dey, B.A. Grzybowski, J.F. Stoddart, Journal of the American Chemical Society 132 (2010) 4310–4320.","mla":"Coskun, Ali, et al. “Molecular-Mechanical Switching at the Nanoparticle−solvent Interface: Practice and Theory.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 12, American Chemical Society, 2010, pp. 4310–20, doi:<a href=\"https://doi.org/10.1021/ja9102327\">10.1021/ja9102327</a>.","chicago":"Coskun, Ali, Paul J. Wesson, Rafal Klajn, Ali Trabolsi, Lei Fang, Mark A. Olson, Sanjeev K. Dey, Bartosz A. Grzybowski, and J. Fraser Stoddart. “Molecular-Mechanical Switching at the Nanoparticle−solvent Interface: Practice and Theory.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja9102327\">https://doi.org/10.1021/ja9102327</a>.","ama":"Coskun A, Wesson PJ, Klajn R, et al. Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. <i>Journal of the American Chemical Society</i>. 2010;132(12):4310-4320. doi:<a href=\"https://doi.org/10.1021/ja9102327\">10.1021/ja9102327</a>","apa":"Coskun, A., Wesson, P. J., Klajn, R., Trabolsi, A., Fang, L., Olson, M. A., … Stoddart, J. F. (2010). Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja9102327\">https://doi.org/10.1021/ja9102327</a>","ieee":"A. Coskun <i>et al.</i>, “Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 12. American Chemical Society, pp. 4310–4320, 2010."},"publisher":"American Chemical Society","intvolume":"       132","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"day":"31","issue":"12","oa_version":"None","abstract":[{"text":"A range (Au, Pt, Pd) of metal nanoparticles (MNPs) has been prepared and functionalized with (a) redox-active stalks containing tetrathiafulvalene (TTF) units, (b) [2]pseudorotaxanes formed between these stalks and cyclobis(paraquat-p-phenylene) (CBPQT4+) rings, and (c) bistable [2]rotaxane molecules where the dumbbell component contains a 1,5-dioxynaphthalene (DNP) unit, as well as a TTF unit, encircled by a CBPQT4+ ring. It transpires that the molecules present in (a) and (c) and the supermolecules described in (b) retain their switching characteristics, previously observed in solution, when they are immobilized onto MNPs. Moreover, their oxidation potentials depend on the fraction, χ, of the molecules or supermolecules on the surface of the nanoparticles. A variation in χ affects the oxidation potentials of the TTF units to the extent that switching can be subjected to fine tuning as a result. Specifically, increasing χ results in positive shifts (i) in the oxidation potentials of the TTF unit in (a)−(c) and (ii) the reduction potentials of the CBPQT4+ rings in (c). These shifts can be attributed to an increase in the electrostatic potential surrounding the MNPs. Both the magnitude and the direction of these shifts are reproduced by a model, based on the Poisson−Boltzmann equation coupled with charge-regulating boundary conditions. Furthermore, the kinetics of relaxation from the metastable state coconformation (MSCC) to the ground-state coconformation (GSCC) of the bistable [2]rotaxane molecules also depends on χ, as well as on the nanoparticle diameter. Increasing either of these parameters accelerates the rate of relaxation from the MSCC to the GSCC. This rate is a function of (i) the activation energy for the relaxation process associated with the bistable [2]rotaxane molecules in solution and (ii) the electrostatic potential surrounding the MNPs. The electrostatic potential depends on (i) the diameter of the MNPs, (ii) the amount of the bistable [2]rotaxane molecules on the surface of the MNPs, and (iii) the equilibrium distribution of the CBPQT4+ rings between the DNP and TTF recognition sites in the GSCC. This electrostatic potential has also been quantified using the Poisson−Boltzmann equation, leading to faithful estimates of the rate constants.","lang":"eng"}],"article_type":"original","article_processing_charge":"No","month":"03","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["20218598"]},"page":"4310-4320","publication":"Journal of the American Chemical Society","date_created":"2023-08-01T09:48:27Z","doi":"10.1021/ja9102327","title":"Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory","language":[{"iso":"eng"}],"extern":"1","date_published":"2010-03-31T00:00:00Z","author":[{"first_name":"Ali","full_name":"Coskun, Ali","last_name":"Coskun"},{"last_name":"Wesson","first_name":"Paul J.","full_name":"Wesson, Paul J."},{"last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal"},{"last_name":"Trabolsi","full_name":"Trabolsi, Ali","first_name":"Ali"},{"full_name":"Fang, Lei","first_name":"Lei","last_name":"Fang"},{"first_name":"Mark A.","full_name":"Olson, Mark A.","last_name":"Olson"},{"first_name":"Sanjeev K.","full_name":"Dey, Sanjeev K.","last_name":"Dey"},{"last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A."},{"full_name":"Stoddart, J. Fraser","first_name":"J. Fraser","last_name":"Stoddart"}],"scopus_import":"1","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"quality_controlled":"1","_id":"13410","date_updated":"2023-08-08T08:00:31Z","type":"journal_article","volume":132},{"volume":6,"date_updated":"2023-08-08T08:15:25Z","_id":"13411","type":"journal_article","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"quality_controlled":"1","status":"public","author":[{"first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"},{"first_name":"Kevin P.","full_name":"Browne, Kevin P.","last_name":"Browne"},{"full_name":"Soh, Siowling","first_name":"Siowling","last_name":"Soh"},{"first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski"}],"scopus_import":"1","date_published":"2010-07-05T00:00:00Z","extern":"1","language":[{"iso":"eng"}],"title":"Nanoparticles that “remember” temperature","doi":"10.1002/smll.200902272","publication":"Small","date_created":"2023-08-01T09:48:38Z","page":"1385-1387","external_id":{"pmid":["20521264"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"article_processing_charge":"No","month":"07","abstract":[{"text":"Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide a basis for sensors that “remember” whether the sample has ever exceeded the melting temperature of the matrix. The operation of these sensors rests on the ability to photoinduce metastable electric dipoles on NP surfaces – upon melting, these dipoles drive NP aggregation, precipitation, and crosslinking. These events are manifested by a pronounced color change.","lang":"eng"}],"article_type":"original","day":"05","issue":"13","oa_version":"None","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"intvolume":"         6","publisher":"Wiley","citation":{"short":"R. Klajn, K.P. Browne, S. Soh, B.A. Grzybowski, Small 6 (2010) 1385–1387.","ista":"Klajn R, Browne KP, Soh S, Grzybowski BA. 2010. Nanoparticles that “remember” temperature. Small. 6(13), 1385–1387.","chicago":"Klajn, Rafal, Kevin P. Browne, Siowling Soh, and Bartosz A. Grzybowski. “Nanoparticles That ‘Remember’ Temperature.” <i>Small</i>. Wiley, 2010. <a href=\"https://doi.org/10.1002/smll.200902272\">https://doi.org/10.1002/smll.200902272</a>.","ama":"Klajn R, Browne KP, Soh S, Grzybowski BA. Nanoparticles that “remember” temperature. <i>Small</i>. 2010;6(13):1385-1387. doi:<a href=\"https://doi.org/10.1002/smll.200902272\">10.1002/smll.200902272</a>","mla":"Klajn, Rafal, et al. “Nanoparticles That ‘Remember’ Temperature.” <i>Small</i>, vol. 6, no. 13, Wiley, 2010, pp. 1385–87, doi:<a href=\"https://doi.org/10.1002/smll.200902272\">10.1002/smll.200902272</a>.","ieee":"R. Klajn, K. P. Browne, S. Soh, and B. A. Grzybowski, “Nanoparticles that ‘remember’ temperature,” <i>Small</i>, vol. 6, no. 13. Wiley, pp. 1385–1387, 2010.","apa":"Klajn, R., Browne, K. P., Soh, S., &#38; Grzybowski, B. A. (2010). Nanoparticles that “remember” temperature. <i>Small</i>. Wiley. <a href=\"https://doi.org/10.1002/smll.200902272\">https://doi.org/10.1002/smll.200902272</a>"},"publication_status":"published","year":"2010"},{"publication":"Chemical Society Reviews","date_created":"2023-08-01T09:49:07Z","external_id":{"pmid":["20407689"]},"page":"2203-2237","title":"Nanoparticles functionalised with reversible molecular and supramolecular switches","doi":"10.1039/b920377j","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","keyword":["General Chemistry"],"status":"public","volume":39,"date_updated":"2023-08-08T08:19:00Z","_id":"13412","type":"journal_article","language":[{"iso":"eng"}],"scopus_import":"1","author":[{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"first_name":"J. Fraser","full_name":"Stoddart, J. Fraser","last_name":"Stoddart"},{"last_name":"Grzybowski","first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A."}],"extern":"1","date_published":"2010-04-21T00:00:00Z","publisher":"Royal Society of Chemistry","citation":{"ista":"Klajn R, Stoddart JF, Grzybowski BA. 2010. Nanoparticles functionalised with reversible molecular and supramolecular switches. Chemical Society Reviews. 39(6), 2203–2237.","short":"R. Klajn, J.F. Stoddart, B.A. Grzybowski, Chemical Society Reviews 39 (2010) 2203–2237.","mla":"Klajn, Rafal, et al. “Nanoparticles Functionalised with Reversible Molecular and Supramolecular Switches.” <i>Chemical Society Reviews</i>, vol. 39, no. 6, Royal Society of Chemistry, 2010, pp. 2203–37, doi:<a href=\"https://doi.org/10.1039/b920377j\">10.1039/b920377j</a>.","ama":"Klajn R, Stoddart JF, Grzybowski BA. Nanoparticles functionalised with reversible molecular and supramolecular switches. <i>Chemical Society Reviews</i>. 2010;39(6):2203-2237. doi:<a href=\"https://doi.org/10.1039/b920377j\">10.1039/b920377j</a>","chicago":"Klajn, Rafal, J. Fraser Stoddart, and Bartosz A. Grzybowski. “Nanoparticles Functionalised with Reversible Molecular and Supramolecular Switches.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2010. <a href=\"https://doi.org/10.1039/b920377j\">https://doi.org/10.1039/b920377j</a>.","apa":"Klajn, R., Stoddart, J. F., &#38; Grzybowski, B. A. (2010). Nanoparticles functionalised with reversible molecular and supramolecular switches. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/b920377j\">https://doi.org/10.1039/b920377j</a>","ieee":"R. Klajn, J. F. Stoddart, and B. A. Grzybowski, “Nanoparticles functionalised with reversible molecular and supramolecular switches,” <i>Chemical Society Reviews</i>, vol. 39, no. 6. Royal Society of Chemistry, pp. 2203–2237, 2010."},"publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"intvolume":"        39","publication_status":"published","year":"2010","pmid":1,"article_type":"original","abstract":[{"text":"Nanoparticles (NPs) and molecular/supramolecular switches have attracted considerable interest during the past decade on account of their unique properties and prominent roles in the fields of organic chemistry and materials science. Materials derived from the combination of these two components are now emerging in the literature. This critical review evaluates materials which comprise NPs functionalised with well-defined self-assembled monolayers of molecular and supramolecular switches. We draw attention to the fact that immobilisation of switches on NPs does not, in general, hamper their switching ability, although it can impart new properties on the supporting particles. This premise leads us to the discussion of systems in which switching on the surfaces of NPs can be used to modulate reversibly a range of NP properties—optical, fluorescent, electrical, magnetic—as well as the controlled release of small molecules. Finally, we discuss examples in which molecular switches direct reversible self-assembly of NPs (308 references).","lang":"eng"}],"oa_version":"None","issue":"6","day":"21","month":"04","article_processing_charge":"No"},{"intvolume":"         5","doi":"10.1186/1745-6150-5-68","license":"https://creativecommons.org/licenses/by/4.0/","title":"Mitochondrial pathogenic mutations are population-specific","publist_id":"6749","citation":{"ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","apa":"Breen, M., &#38; Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010).","ista":"Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.","chicago":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>.","ama":"Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>","mla":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>."},"publisher":"BioMed Central","date_created":"2018-12-11T11:49:06Z","publication":"Biology Direct","acknowledgement":"We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.","year":"2010","publication_status":"published","type":"journal_article","_id":"901","date_updated":"2021-01-12T08:21:46Z","volume":5,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":0,"date_published":"2010-12-31T00:00:00Z","extern":1,"month":"12","author":[{"last_name":"Breen","first_name":"Michael","full_name":"Breen, Michael S"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"day":"31","abstract":[{"lang":"eng","text":"Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst)."}]},{"date_updated":"2023-02-23T13:46:40Z","_id":"9012","type":"journal_article","volume":104,"status":"public","quality_controlled":"1","date_published":"2010-04-02T00:00:00Z","extern":"1","scopus_import":"1","author":[{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"},{"last_name":"Abécassis","full_name":"Abécassis, Benjamin","first_name":"Benjamin"},{"last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile"},{"last_name":"Ybert","full_name":"Ybert, Christophe","first_name":"Christophe"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.104.138302","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","external_id":{"arxiv":["1004.1256 "],"pmid":["20481918"]},"publication":"Physical Review Letters","date_created":"2021-01-19T10:25:04Z","article_number":"138302","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","pmid":1,"month":"04","article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","day":"02","issue":"13","article_type":"letter_note","abstract":[{"text":"In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.","lang":"eng"}],"intvolume":"       104","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"citation":{"apa":"Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>","ieee":"J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Colloidal motility and pattern formation under rectified diffusiophoresis,” <i>Physical Review Letters</i>, vol. 104, no. 13. American Physical Society, 2010.","ista":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal motility and pattern formation under rectified diffusiophoresis. Physical Review Letters. 104(13), 138302.","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010).","mla":"Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>, vol. 104, no. 13, 138302, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>.","chicago":"Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>.","ama":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. 2010;104(13). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>"},"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"year":"2010","publication_status":"published","oa":1},{"pmid":1,"arxiv":1,"month":"08","article_processing_charge":"No","article_type":"letter_note","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"}],"oa_version":"Preprint","day":"20","issue":"8","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"intvolume":"       105","publisher":"American Physical Society ","citation":{"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>.","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>","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>.","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.","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>","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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.4340"}],"publication_status":"published","oa":1,"year":"2010","volume":105,"date_updated":"2023-02-23T13:46:42Z","_id":"9013","type":"journal_article","quality_controlled":"1","status":"public","scopus_import":"1","author":[{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"},{"last_name":"Cottin-Bizonne","first_name":"Cécile","full_name":"Cottin-Bizonne, Cécile"},{"last_name":"Ybert","first_name":"Christophe","full_name":"Ybert, Christophe"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"date_published":"2010-08-20T00:00:00Z","extern":"1","language":[{"iso":"eng"}],"title":"Sedimentation and effective temperature of active colloidal suspensions","doi":"10.1103/physrevlett.105.088304","date_created":"2021-01-19T10:26:33Z","publication":"Physical Review Letters","article_number":"088304","external_id":{"arxiv":["1004.4340"],"pmid":["20868136"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"author":[{"last_name":"Canuto","first_name":"V.M.","full_name":"Canuto, V.M."},{"full_name":"Howard, A.M.","first_name":"A.M.","last_name":"Howard"},{"full_name":"Cheng, Y.","first_name":"Y.","last_name":"Cheng"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J"},{"last_name":"Leboissetier","full_name":"Leboissetier, A.","first_name":"A."},{"last_name":"Jayne","full_name":"Jayne, S.R.","first_name":"S.R."}],"month":"05","extern":"1","date_published":"2010-05-12T00:00:00Z","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well.\r\n\r\nAs for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve.","lang":"eng"}],"oa_version":"None","issue":"3-4","day":"12","volume":34,"_id":"9145","date_updated":"2022-01-24T13:51:35Z","type":"journal_article","quality_controlled":"1","keyword":["Computer Science (miscellaneous)","Geotechnical Engineering and Engineering Geology","Atmospheric Science","Oceanography"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","year":"2010","publication_identifier":{"issn":["1463-5003"]},"title":"Ocean turbulence, III: New GISS vertical mixing scheme","doi":"10.1016/j.ocemod.2010.04.006","intvolume":"        34","date_created":"2021-02-15T14:40:19Z","publication":"Ocean Modelling","publisher":"Elsevier","citation":{"ista":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010. Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4), 70–91.","short":"V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne, Ocean Modelling 34 (2010) 70–91.","mla":"Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>.","chicago":"Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier, and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>.","ama":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. 2010;34(3-4):70-91. doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>","apa":"Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A., &#38; Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>","ieee":"V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” <i>Ocean Modelling</i>, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010."},"page":"70-91"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1088/1748-9326/5/2/025207","title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","article_number":"025207","date_created":"2021-02-15T14:40:46Z","publication":"Environmental Research Letters","extern":"1","date_published":"2010-04-09T00:00:00Z","author":[{"last_name":"O’Gorman","full_name":"O’Gorman, P A","first_name":"P A"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"9146","date_updated":"2022-01-24T13:51:02Z","volume":5,"status":"public","keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/5/2/025207","open_access":"1"}],"year":"2010","oa":1,"publication_status":"published","intvolume":"         5","publication_identifier":{"issn":["1748-9326"]},"citation":{"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>.","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>.","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>","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.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","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>","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."},"publisher":"IOP Publishing","article_processing_charge":"No","month":"04","day":"09","issue":"2","oa_version":"Published Version","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"}],"article_type":"original"},{"article_processing_charge":"No","extern":"1","date_published":"2010-04-23T00:00:00Z","month":"04","author":[{"first_name":"Thomas","full_name":"Angelini, Thomas","last_name":"Angelini"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trepat, Xavier","first_name":"Xavier","last_name":"Trepat"},{"full_name":"Fredberg, Jeffrey","first_name":"Jeffrey","last_name":"Fredberg"},{"first_name":"David","full_name":"Weitz, David","last_name":"Weitz"}],"issue":"16","day":"23","oa_version":"None","abstract":[{"lang":"eng","text":"Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration."}],"language":[{"iso":"eng"}],"_id":"920","date_updated":"2021-01-12T08:21:55Z","type":"journal_article","volume":104,"status":"public","acknowledgement":"This work was supported by the NSF (DMR-0602684) and the Harvard MRSEC (DMR-0820484).\r\nWe would like to thank Dr. James Butler for helpful conversations.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2010","publication_status":"published","intvolume":"       104","doi":"10.1103/PhysRevLett.104.168104","title":"Cell migration driven by cooperative substrate deformation patterns","publist_id":"6523","citation":{"apa":"Angelini, T., Hannezo, E. B., Trepat, X., Fredberg, J., &#38; Weitz, D. (2010). Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>","ieee":"T. Angelini, E. B. Hannezo, X. Trepat, J. Fredberg, and D. Weitz, “Cell migration driven by cooperative substrate deformation patterns,” <i>Physical Review Letters</i>, vol. 104, no. 16. American Physical Society, 2010.","ista":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. 2010. Cell migration driven by cooperative substrate deformation patterns. Physical Review Letters. 104(16).","short":"T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review Letters 104 (2010).","mla":"Angelini, Thomas, et al. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>, vol. 104, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>.","chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepat, Jeffrey Fredberg, and David Weitz. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>.","ama":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. 2010;104(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>"},"publisher":"American Physical Society","publication":"Physical Review Letters","date_created":"2018-12-11T11:49:12Z"},{"publication":"Science","date_created":"2021-06-04T08:26:08Z","external_id":{"pmid":["20395474 "]},"page":"916-919","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","doi":"10.1126/science.1186366","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","keyword":["Multidisciplinary"],"status":"public","volume":328,"date_updated":"2021-12-14T08:35:37Z","_id":"9452","type":"journal_article","language":[{"iso":"eng"}],"scopus_import":"1","author":[{"full_name":"Zemach, Assaf ","first_name":"Assaf ","last_name":"Zemach"},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"last_name":"Silva","full_name":"Silva, Pedro","first_name":"Pedro"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"date_published":"2010-05-14T00:00:00Z","extern":"1","publisher":"American Association for the Advancement of Science","citation":{"ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919."},"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"intvolume":"       328","publication_status":"published","year":"2010","pmid":1,"article_type":"original","abstract":[{"lang":"eng","text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes."}],"oa_version":"None","day":"14","issue":"5980","department":[{"_id":"DaZi"}],"month":"05","article_processing_charge":"No"},{"publisher":"National Academy of Sciences","citation":{"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.","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.","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>.","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>","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>.","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>","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."},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":"       107","publication_status":"published","oa":1,"year":"2010","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1009695107"}],"pmid":1,"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."}],"article_type":"original","day":"26","issue":"43","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"DaZi"}],"month":"10","publication":"Proceedings of the National Academy of Sciences","date_created":"2021-06-07T09:31:01Z","external_id":{"pmid":["20937895"]},"page":"18729-18734","title":"Local DNA hypomethylation activates genes in rice endosperm","doi":"10.1073/pnas.1009695107","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","status":"public","volume":107,"type":"journal_article","_id":"9485","date_updated":"2021-12-14T08:40:02Z","language":[{"iso":"eng"}],"author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Silva","full_name":"Silva, Pedro","first_name":"Pedro"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"full_name":"Dotson, Bradley","first_name":"Bradley","last_name":"Dotson"},{"full_name":"Brooks, Matthew D.","first_name":"Matthew D.","last_name":"Brooks"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"scopus_import":"1","extern":"1","date_published":"2010-10-26T00:00:00Z"},{"language":[{"iso":"eng"}],"scopus_import":"1","author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"date_published":"2010-09-14T00:00:00Z","extern":"1","quality_controlled":"1","status":"public","volume":20,"_id":"9489","type":"journal_article","date_updated":"2021-12-14T08:52:34Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Current Biology","date_created":"2021-06-07T09:45:27Z","external_id":{"pmid":["20833323"]},"page":"R780-R785","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","doi":"10.1016/j.cub.2010.07.007","article_type":"review","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."}],"oa_version":"Published Version","issue":"17","day":"14","month":"09","department":[{"_id":"DaZi"}],"article_processing_charge":"No","pmid":1,"publication_status":"published","oa":1,"year":"2010","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"publisher":"Elsevier","citation":{"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.","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>","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>","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>.","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>.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785."},"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"intvolume":"        20"},{"date_published":"2010-12-23T00:00:00Z","extern":"1","author":[{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Cacciuto","full_name":"Cacciuto, Angelo","first_name":"Angelo"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"10127","date_updated":"2021-10-12T09:49:27Z","volume":7,"status":"public","keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.","doi":"10.1039/c0sm01143f","title":"Particle self-assembly on soft elastic shells","page":"1874-1878","external_id":{"arxiv":["1010.2453"]},"date_created":"2021-10-12T08:34:23Z","publication":"Soft Matter","article_processing_charge":"No","month":"12","arxiv":1,"issue":"5","day":"23","oa_version":"Preprint","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"}],"article_type":"original","main_file_link":[{"url":"https://arxiv.org/abs/1010.2453","open_access":"1"}],"year":"2010","oa":1,"publication_status":"published","intvolume":"         7","publication_identifier":{"issn":["1744-683X","1744-6848"]},"citation":{"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>","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.","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.","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>.","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>","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>."},"publisher":"Royal Society of Chemistry (RSC)"},{"publisher":"Royal Society of Chemistry ","citation":{"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>","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>.","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>.","short":"A. Šarić, T. Hrenar, M. Mališ, N. Došlić, Physical Chemistry Chemical Physics 12 (2010) 4678–4685.","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.","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>"},"publication_identifier":{"issn":["1463-9076","1463-9084"]},"intvolume":"        12","publication_status":"published","year":"2010","main_file_link":[{"url":"https://europepmc.org/article/med/20428547"}],"pmid":1,"article_type":"original","abstract":[{"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.","lang":"eng"}],"oa_version":"None","day":"16","issue":"18","month":"03","article_processing_charge":"No","date_created":"2021-10-12T08:44:34Z","publication":"Physical Chemistry Chemical Physics","external_id":{"pmid":["20428547"]},"page":"4678-4685","title":"Quantum mechanical study of secondary structure formation in protected dipeptides","doi":"10.1039/b923041f","acknowledgement":"This work has been supported by the MZOŠ projects 098-0352851-2921 and 119-1191342-2959.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","quality_controlled":"1","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"status":"public","volume":12,"_id":"10128","date_updated":"2021-10-12T09:49:22Z","type":"journal_article","language":[{"iso":"eng"}],"author":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"last_name":"Hrenar","first_name":"T.","full_name":"Hrenar, T."},{"last_name":"Mališ","full_name":"Mališ, M.","first_name":"M."},{"last_name":"Došlić","full_name":"Došlić, N.","first_name":"N."}],"extern":"1","date_published":"2010-03-16T00:00:00Z"},{"issue":"22","day":"15","oa_version":"Preprint","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"}],"article_type":"original","article_processing_charge":"No","month":"10","arxiv":1,"pmid":1,"year":"2010","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1010.2458"}],"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>.","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>","ista":"Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 115(22), 7182–7189.","short":"A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115 (2010) 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>","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."},"publisher":"American Chemical Society","intvolume":"       115","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"language":[{"iso":"eng"}],"extern":"1","date_published":"2010-10-15T00:00:00Z","author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Bozorgui","first_name":"Behnaz","full_name":"Bozorgui, Behnaz"},{"last_name":"Cacciuto","full_name":"Cacciuto, Angelo","first_name":"Angelo"}],"scopus_import":"1","status":"public","keyword":["materials chemistry"],"quality_controlled":"1","date_updated":"2021-11-29T16:20:29Z","_id":"10390","type":"journal_article","volume":115,"acknowledgement":"This work was supported by the National Science Foundation under CAREER Grant No. DMR-0846426 and partly by Columbia University.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["20949934"],"arxiv":["1010.2458"]},"page":"7182-7189","date_created":"2021-11-29T15:13:17Z","publication":"The Journal of Physical Chemistry B","doi":"10.1021/jp107545w","title":"Packing of soft asymmetric dumbbells"}]