[{"date_updated":"2021-01-12T06:53:07Z","intvolume":"       105","date_created":"2018-12-11T11:53:56Z","issue":"16","quality_controlled":0,"publisher":"American Physical Society","author":[{"last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Johannes Fink"},{"last_name":"Steffen","full_name":"Steffen, L. Kraig","first_name":"L."},{"last_name":"Studer","first_name":"Peter","full_name":"Studer, Peter"},{"first_name":"Lev","full_name":"Bishop, Lev S","last_name":"Bishop"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"full_name":"Bianchetti, R","first_name":"R","last_name":"Bianchetti"},{"first_name":"Deniz","full_name":"Bozyigit, Deniz","last_name":"Bozyigit"},{"first_name":"C","full_name":"Lang, C","last_name":"Lang"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"last_name":"Leek","first_name":"Peter","full_name":"Leek, Peter J"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"}],"date_published":"2010-10-14T00:00:00Z","abstract":[{"lang":"eng","text":"The quantum properties of electromagnetic, mechanical or other harmonic oscillators can be revealed by investigating their strong coherent coupling to a single quantum two level system in an approach known as cavity quantum electrodynamics (QED). At temperatures much lower than the characteristic energy level spacing the observation of vacuum Rabi oscillations or mode splittings with one or a few quanta asserts the quantum nature of the oscillator. Here, we study how the classical response of a cavity QED system emerges from the quantum one when its thermal occupation-or effective temperature-is raised gradually over 5 orders of magnitude. In this way we explore in detail the continuous quantum-to-classical crossover and demonstrate how to extract effective cavity field temperatures from both spectroscopic and time-resolved vacuum Rabi measurements."}],"publist_id":"5343","extern":1,"day":"14","type":"journal_article","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1003.1161","open_access":"1"}],"month":"10","title":"Quantum-to-classical transition in cavity quantum electrodynamics","_id":"1773","publication":"Physical Review Letters","volume":105,"doi":"10.1103/PhysRevLett.105.163601","publication_status":"published","year":"2010","oa":1,"acknowledgement":"This work was supported by SNF, EuroSQIP and ETHZ. L. S. B. acknowledges support by LPS/NSA under ARO contract No. W911NF-05-1-0365 and the NSF under grant No. DMR-0653377","citation":{"ieee":"J. M. Fink <i>et al.</i>, “Quantum-to-classical transition in cavity quantum electrodynamics,” <i>Physical Review Letters</i>, vol. 105, no. 16. American Physical Society, 2010.","ama":"Fink JM, Steffen L, Studer P, et al. Quantum-to-classical transition in cavity quantum electrodynamics. <i>Physical Review Letters</i>. 2010;105(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">10.1103/PhysRevLett.105.163601</a>","chicago":"Fink, Johannes M, L. Steffen, Peter Studer, Lev Bishop, Matthias Baur, R Bianchetti, Deniz Bozyigit, et al. “Quantum-to-Classical Transition in Cavity Quantum Electrodynamics.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">https://doi.org/10.1103/PhysRevLett.105.163601</a>.","mla":"Fink, Johannes M., et al. “Quantum-to-Classical Transition in Cavity Quantum Electrodynamics.” <i>Physical Review Letters</i>, vol. 105, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">10.1103/PhysRevLett.105.163601</a>.","apa":"Fink, J. M., Steffen, L., Studer, P., Bishop, L., Baur, M., Bianchetti, R., … Wallraff, A. (2010). Quantum-to-classical transition in cavity quantum electrodynamics. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.105.163601\">https://doi.org/10.1103/PhysRevLett.105.163601</a>","short":"J.M. Fink, L. Steffen, P. Studer, L. Bishop, M. Baur, R. Bianchetti, D. Bozyigit, C. Lang, S. Filipp, P. Leek, A. Wallraff, Physical Review Letters 105 (2010).","ista":"Fink JM, Steffen L, Studer P, Bishop L, Baur M, Bianchetti R, Bozyigit D, Lang C, Filipp S, Leek P, Wallraff A. 2010. Quantum-to-classical transition in cavity quantum electrodynamics. Physical Review Letters. 105(16)."}},{"citation":{"short":"R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, C. Lang, L. Steffen, M. Boissonneault, A. Blais, A. Wallraff, Physical Review Letters 105 (2010).","ista":"Bianchetti R, Filipp S, Baur M, Fink JM, Lang C, Steffen L, Boissonneault M, Blais A, Wallraff A. 2010. Control and tomography of a three level superconducting artificial atom. Physical Review Letters. 105(22).","apa":"Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Lang, C., Steffen, L., … Wallraff, A. (2010). Control and tomography of a three level superconducting artificial atom. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">https://doi.org/10.1103/PhysRevLett.105.223601</a>","mla":"Bianchetti, R., et al. “Control and Tomography of a Three Level Superconducting Artificial Atom.” <i>Physical Review Letters</i>, vol. 105, no. 22, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">10.1103/PhysRevLett.105.223601</a>.","ieee":"R. Bianchetti <i>et al.</i>, “Control and tomography of a three level superconducting artificial atom,” <i>Physical Review Letters</i>, vol. 105, no. 22. American Physical Society, 2010.","ama":"Bianchetti R, Filipp S, Baur M, et al. Control and tomography of a three level superconducting artificial atom. <i>Physical Review Letters</i>. 2010;105(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">10.1103/PhysRevLett.105.223601</a>","chicago":"Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, C Lang, L. Steffen, Maxime Boissonneault, Alexandre Blais, and Andreas Wallraff. “Control and Tomography of a Three Level Superconducting Artificial Atom.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.105.223601\">https://doi.org/10.1103/PhysRevLett.105.223601</a>."},"acknowledgement":"This work was supported by SNF, ETHZ, the Austrian Science Foundation (FWF), and the EU projects SOLID and GEOMDISS. A. B. is supported by NSERC, the Alfred P. Sloan Foundation, and CIFAR","oa":1,"year":"2010","publication_status":"published","doi":"10.1103/PhysRevLett.105.223601","_id":"1774","volume":105,"publication":"Physical Review Letters","title":"Control and tomography of a three level superconducting artificial atom","month":"11","main_file_link":[{"url":"http://arxiv.org/abs/1004.5504","open_access":"1"}],"status":"public","type":"journal_article","day":"24","extern":1,"publist_id":"5341","abstract":[{"text":"A number of superconducting qubits, such as the transmon or the phase qubit, have an energy level structure with small anharmonicity. This allows for convenient access of higher excited states with similar frequencies. However, special care has to be taken to avoid unwanted higher-level populations when using short control pulses. Here we demonstrate the preparation of arbitrary three level superposition states using optimal control techniques in a transmon. Performing dispersive readout, we extract the populations of all three levels of the qutrit and study the coherence of its excited states. Finally we demonstrate full quantum state tomography of the prepared qutrit states and evaluate the fidelities of a set of states, finding on average 95%.","lang":"eng"}],"date_published":"2010-11-24T00:00:00Z","quality_controlled":0,"author":[{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"last_name":"Lang","full_name":"Lang, C","first_name":"C"},{"last_name":"Steffen","full_name":"Steffen, L. Kraig","first_name":"L."},{"first_name":"Maxime","full_name":"Boissonneault, Maxime","last_name":"Boissonneault"},{"last_name":"Blais","full_name":"Blais, Alexandre","first_name":"Alexandre"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}],"publisher":"American Physical Society","issue":"22","intvolume":"       105","date_created":"2018-12-11T11:53:56Z","date_updated":"2021-01-12T06:53:07Z"},{"date_updated":"2021-01-12T06:53:17Z","date_created":"2018-12-11T11:54:05Z","intvolume":"       329","issue":"5990","publisher":"American Association for the Advancement of Science","quality_controlled":0,"author":[{"last_name":"Busskamp","first_name":"Volker","full_name":"Busskamp, Volker"},{"last_name":"Duebel","first_name":"Jens","full_name":"Duebel, Jens"},{"full_name":"Bálya, Dávid","first_name":"Dávid","last_name":"Bálya"},{"first_name":"Mathias","full_name":"Fradot, Mathias","last_name":"Fradot"},{"last_name":"Viney","full_name":"Viney, Tim J","first_name":"Tim"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Sandra Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"},{"last_name":"Groner","full_name":"Groner, Anna C","first_name":"Anna"},{"last_name":"Cabuy","first_name":"Erik","full_name":"Cabuy, Erik"},{"last_name":"Forster","first_name":"Valérie","full_name":"Forster, Valérie"},{"full_name":"Seeliger, Mathias W","first_name":"Mathias","last_name":"Seeliger"},{"full_name":"Biel, Martin","first_name":"Martin","last_name":"Biel"},{"full_name":"Humphries, Peter","first_name":"Peter","last_name":"Humphries"},{"last_name":"Pâques","first_name":"Michel","full_name":"Pâques, Michel"},{"last_name":"Mohand Saïd","first_name":"Saddek","full_name":"Mohand-Saïd, Saddek"},{"last_name":"Trono","full_name":"Trono, Didier","first_name":"Didier"},{"full_name":"Deisseroth, Karl A","first_name":"Karl","last_name":"Deisseroth"},{"last_name":"Sähel","first_name":"José","full_name":"Sähel, José A"},{"first_name":"Serge","full_name":"Picaud, Serge A","last_name":"Picaud"},{"last_name":"Roska","full_name":"Roska, Botond M","first_name":"Botond"}],"date_published":"2010-07-23T00:00:00Z","abstract":[{"lang":"eng","text":"Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy."}],"publist_id":"5310","day":"23","extern":1,"type":"journal_article","status":"public","month":"07","page":"413 - 417","_id":"1800","title":"Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa","publication":"Science","volume":329,"doi":"10.1126/science.1190897","publication_status":"published","year":"2010","acknowledgement":"This study was supported by Friedrich Miescher Institute funds; a U.S. Office of Naval Research Naval International Cooperative Opportunities in Science and Technology Program grant; a Marie Curie Excellence grant and a European Union (EU) HEALTH-F2-223156 grant to B.R.; a grant from the EU (RETICIRC) to B.R. and S.P.; grants from the Agence nationale de la recherche (MEDINAS, RETINE) to S.P.; a Center Grant from Foundation Fighting Blindness (U.S.) to S.M.-S. and J.A.S.; grants from the Swiss National Science Foundation and the EU to D.T.; a grant from the EU (TREATRUSH) to J.A.S., S.P., and B.R.; a Marie Curie Postdoctoral Fellowship to D.B.; and a National Centers of Competence in Research Frontiers in Genetics fellowship to V.B. and A.C.G. The Ocular Genetics Unit at Trinity College Dublin is supported by Science Foundation Ireland","citation":{"apa":"Busskamp, V., Duebel, J., Bálya, D., Fradot, M., Viney, T., Siegert, S., … Roska, B. (2010). Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1190897\">https://doi.org/10.1126/science.1190897</a>","mla":"Busskamp, Volker, et al. “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa.” <i>Science</i>, vol. 329, no. 5990, American Association for the Advancement of Science, 2010, pp. 413–17, doi:<a href=\"https://doi.org/10.1126/science.1190897\">10.1126/science.1190897</a>.","ista":"Busskamp V, Duebel J, Bálya D, Fradot M, Viney T, Siegert S, Groner A, Cabuy E, Forster V, Seeliger M, Biel M, Humphries P, Pâques M, Mohand Saïd S, Trono D, Deisseroth K, Sähel J, Picaud S, Roska B. 2010. Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. Science. 329(5990), 413–417.","short":"V. Busskamp, J. Duebel, D. Bálya, M. Fradot, T. Viney, S. Siegert, A. Groner, E. Cabuy, V. Forster, M. Seeliger, M. Biel, P. Humphries, M. Pâques, S. Mohand Saïd, D. Trono, K. Deisseroth, J. Sähel, S. Picaud, B. Roska, Science 329 (2010) 413–417.","chicago":"Busskamp, Volker, Jens Duebel, Dávid Bálya, Mathias Fradot, Tim Viney, Sandra Siegert, Anna Groner, et al. “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1190897\">https://doi.org/10.1126/science.1190897</a>.","ama":"Busskamp V, Duebel J, Bálya D, et al. Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa. <i>Science</i>. 2010;329(5990):413-417. doi:<a href=\"https://doi.org/10.1126/science.1190897\">10.1126/science.1190897</a>","ieee":"V. Busskamp <i>et al.</i>, “Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa,” <i>Science</i>, vol. 329, no. 5990. American Association for the Advancement of Science, pp. 413–417, 2010."}},{"acknowledgement":"This work was funded by the Medical Research Council.","citation":{"chicago":"Efremov, Rouslan, Rozbeh Baradaran, and Leonid A Sazanov. “The Architecture of Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09066\">https://doi.org/10.1038/nature09066</a>.","ieee":"R. Efremov, R. Baradaran, and L. A. Sazanov, “The architecture of respiratory complex I,” <i>Nature</i>, vol. 465, no. 7297. Nature Publishing Group, pp. 441–445, 2010.","ama":"Efremov R, Baradaran R, Sazanov LA. The architecture of respiratory complex I. <i>Nature</i>. 2010;465(7297):441-445. doi:<a href=\"https://doi.org/10.1038/nature09066\">10.1038/nature09066</a>","ista":"Efremov R, Baradaran R, Sazanov LA. 2010. The architecture of respiratory complex I. Nature. 465(7297), 441–445.","short":"R. Efremov, R. Baradaran, L.A. Sazanov, Nature 465 (2010) 441–445.","mla":"Efremov, Rouslan, et al. “The Architecture of Respiratory Complex I.” <i>Nature</i>, vol. 465, no. 7297, Nature Publishing Group, 2010, pp. 441–45, doi:<a href=\"https://doi.org/10.1038/nature09066\">10.1038/nature09066</a>.","apa":"Efremov, R., Baradaran, R., &#38; Sazanov, L. A. (2010). The architecture of respiratory complex I. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09066\">https://doi.org/10.1038/nature09066</a>"},"_id":"1970","publication":"Nature","volume":465,"title":"The architecture of respiratory complex I","year":"2010","publication_status":"published","doi":"10.1038/nature09066","page":"441 - 445","month":"05","day":"27","extern":1,"type":"journal_article","status":"public","abstract":[{"lang":"eng","text":"Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the α-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 Å resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-Å long amphipathic α-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 Å resolution. The L-shaped assembly consists of the α-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic α-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation."}],"publist_id":"5113","author":[{"first_name":"Rouslan","full_name":"Efremov, Rouslan G","last_name":"Efremov"},{"full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh","last_name":"Baradaran"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Leonid Sazanov","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"publisher":"Nature Publishing Group","quality_controlled":0,"date_published":"2010-05-27T00:00:00Z","intvolume":"       465","date_created":"2018-12-11T11:54:58Z","date_updated":"2021-01-12T06:54:25Z","issue":"7297"},{"date_created":"2023-08-01T09:48:11Z","quality_controlled":"1","publisher":"De Gruyter","abstract":[{"lang":"eng","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."}],"extern":"1","day":"15","type":"journal_article","status":"public","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1351/pac-con-10-09-04"}],"month":"10","page":"2247-2279","publication_identifier":{"issn":["0033-4545"],"eissn":["1365-3075"]},"volume":82,"language":[{"iso":"eng"}],"year":"2010","date_updated":"2023-08-08T07:58:13Z","intvolume":"        82","issue":"12","author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"}],"date_published":"2010-10-15T00:00:00Z","oa_version":"Published Version","scopus_import":"1","keyword":["General Chemical Engineering","General Chemistry"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Immobilized azobenzenes for the construction of photoresponsive materials","_id":"13409","publication":"Pure and Applied Chemistry","article_processing_charge":"No","doi":"10.1351/pac-con-10-09-04","publication_status":"published","oa":1,"citation":{"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.","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>.","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>","ista":"Klajn R. 2010. Immobilized azobenzenes for the construction of photoresponsive materials. Pure and Applied Chemistry. 82(12), 2247–2279.","short":"R. Klajn, Pure and Applied Chemistry 82 (2010) 2247–2279."}},{"oa_version":"None","scopus_import":"1","issue":"12","date_updated":"2023-08-08T08:00:31Z","intvolume":"       132","date_published":"2010-03-31T00:00:00Z","author":[{"last_name":"Coskun","full_name":"Coskun, Ali","first_name":"Ali"},{"full_name":"Wesson, Paul J.","first_name":"Paul J.","last_name":"Wesson"},{"last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal"},{"full_name":"Trabolsi, Ali","first_name":"Ali","last_name":"Trabolsi"},{"last_name":"Fang","full_name":"Fang, Lei","first_name":"Lei"},{"last_name":"Olson","first_name":"Mark A.","full_name":"Olson, Mark A."},{"first_name":"Sanjeev K.","full_name":"Dey, Sanjeev K.","last_name":"Dey"},{"first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski"},{"first_name":"J. Fraser","full_name":"Stoddart, J. Fraser","last_name":"Stoddart"}],"doi":"10.1021/ja9102327","publication_status":"published","_id":"13410","article_processing_charge":"No","title":"Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory","publication":"Journal of the American Chemical Society","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.","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>","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>.","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.","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>"},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"type":"journal_article","status":"public","day":"31","extern":"1","date_created":"2023-08-01T09:48:27Z","external_id":{"pmid":["20218598"]},"publisher":"American Chemical Society","quality_controlled":"1","language":[{"iso":"eng"}],"year":"2010","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"volume":132,"article_type":"original","month":"03","page":"4310-4320","pmid":1},{"month":"07","article_type":"original","page":"1385-1387","pmid":1,"year":"2010","language":[{"iso":"eng"}],"volume":6,"publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"date_created":"2023-08-01T09:48:38Z","quality_controlled":"1","publisher":"Wiley","external_id":{"pmid":["20521264"]},"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"}],"type":"journal_article","status":"public","day":"05","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"publication_status":"published","doi":"10.1002/smll.200902272","_id":"13411","publication":"Small","title":"Nanoparticles that “remember” temperature","article_processing_charge":"No","citation":{"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>.","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>","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.","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>","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.","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>."},"issue":"13","intvolume":"         6","date_updated":"2023-08-08T08:15:25Z","date_published":"2010-07-05T00:00:00Z","author":[{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"first_name":"Kevin P.","full_name":"Browne, Kevin P.","last_name":"Browne"},{"last_name":"Soh","first_name":"Siowling","full_name":"Soh, Siowling"},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"oa_version":"None","scopus_import":"1"},{"intvolume":"        39","date_updated":"2023-08-08T08:19:00Z","issue":"6","author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"},{"last_name":"Stoddart","full_name":"Stoddart, J. Fraser","first_name":"J. Fraser"},{"last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A."}],"date_published":"2010-04-21T00:00:00Z","oa_version":"None","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Chemistry"],"title":"Nanoparticles functionalised with reversible molecular and supramolecular switches","_id":"13412","article_processing_charge":"No","publication":"Chemical Society Reviews","publication_status":"published","doi":"10.1039/b920377j","citation":{"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>.","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>","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.","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>","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.","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>."},"date_created":"2023-08-01T09:49:07Z","publisher":"Royal Society of Chemistry","quality_controlled":"1","external_id":{"pmid":["20407689"]},"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"}],"extern":"1","day":"21","type":"journal_article","status":"public","month":"04","article_type":"original","pmid":1,"page":"2203-2237","volume":39,"publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"year":"2010","language":[{"iso":"eng"}]},{"date_published":"2010-07-01T00:00:00Z","quality_controlled":0,"publisher":"Springer","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel","last_name":"Hausel"}],"issue":"1","date_updated":"2021-01-12T06:50:56Z","date_created":"2018-12-11T11:52:11Z","intvolume":"       181","status":"public","type":"journal_article","day":"01","extern":1,"publist_id":"5730","abstract":[{"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.","lang":"eng"}],"page":"21 - 37","main_file_link":[{"url":"http://arxiv.org/abs/0811.1569","open_access":"1"}],"month":"07","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>.","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>","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.","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>.","ieee":"T. Hausel, “Kac’s conjecture from Nakajima quiver varieties,” <i>Inventiones Mathematicae</i>, vol. 181, no. 1. Springer, pp. 21–37, 2010.","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>"},"oa":1,"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.","doi":"10.1007/s00222-010-0241-3","year":"2010","publication_status":"published","_id":"1465","title":"Kac's conjecture from Nakajima quiver varieties","publication":"Inventiones Mathematicae","volume":181},{"page":"131 - 135","month":"02","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0905.3491"}],"citation":{"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>.","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.","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>","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>","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>.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Comptes Rendus Mathematique 348 (2010) 131–135.","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."},"oa":1,"publication_status":"published","year":"2010","doi":"10.1016/j.crma.2010.01.025","title":"Topology of character varieties and representations of quivers","_id":"1466","publication":"Comptes Rendus Mathematique","volume":348,"date_published":"2010-02-01T00:00:00Z","quality_controlled":0,"publisher":"Elsevier","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel","last_name":"Hausel"},{"last_name":"Letellier","full_name":"Letellier, Emmanuel","first_name":"Emmanuel"},{"last_name":"Rodríguez Villegas","first_name":"Fernando","full_name":"Rodríguez Villegas, Fernando"}],"issue":"3-4","intvolume":"       348","date_created":"2018-12-11T11:52:11Z","date_updated":"2021-01-12T06:50:56Z","status":"public","type":"journal_article","day":"01","extern":1,"publist_id":"5731","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]."}]},{"title":"S-Duality in HyperkäHler Hodge Theory","_id":"1468","publication":"The Many Facets of Geometry: A Tribute to Nigel Hitchin","year":"2010","publication_status":"published","doi":"10.1093/acprof:oso/9780199534920.003.0016","oa":1,"citation":{"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.","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>","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>.","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>.","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.","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>"},"month":"09","main_file_link":[{"url":"http://arxiv.org/abs/0709.0504","open_access":"1"}],"abstract":[{"lang":"eng","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?"}],"publist_id":"5729","day":"01","extern":1,"type":"book_chapter","status":"public","date_created":"2018-12-11T11:52:12Z","date_updated":"2021-01-12T06:50:57Z","quality_controlled":0,"publisher":"Oxford University Press","author":[{"last_name":"Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel"}],"date_published":"2010-09-01T00:00:00Z"},{"date_published":"2010-10-07T00:00:00Z","publisher":"IST Austria","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna"},{"first_name":"Rohit","full_name":"Singh, Rohit","last_name":"Singh"}],"date_created":"2018-12-12T11:39:03Z","date_updated":"2023-02-23T11:24:08Z","status":"public","type":"technical_report","file_date_updated":"2020-07-14T12:46:42Z","day":"07","related_material":{"record":[{"relation":"later_version","status":"public","id":"3366"}]},"alternative_title":["IST Austria Technical Report"],"pubrep_id":"24","ddc":["000","005"],"has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements.","lang":"eng"}],"page":"17","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>."},"oa":1,"year":"2010","file":[{"file_name":"IST-2010-0004_IST-2010-0004.pdf","file_id":"5515","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T11:53:53Z","date_updated":"2020-07-14T12:46:42Z","checksum":"da38782d2388a6fa32109d10bb9bad67","file_size":429101,"creator":"system"}],"publication_status":"published","doi":"10.15479/AT:IST-2010-0004","language":[{"iso":"eng"}],"title":"Quantitative synthesis for concurrent programs","_id":"5388","publication_identifier":{"issn":["2664-1690"]}},{"date_published":"2010-06-04T00:00:00Z","publisher":"IST Austria","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","full_name":"Cerny, Pavol","last_name":"Cerny"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"}],"date_updated":"2023-02-23T12:09:16Z","date_created":"2018-12-12T11:39:03Z","status":"public","type":"technical_report","related_material":{"record":[{"relation":"later_version","id":"3249","status":"public"},{"id":"4393","status":"public","relation":"later_version"}]},"alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:42Z","day":"04","oa_version":"Published Version","has_accepted_license":"1","ddc":["005"],"pubrep_id":"25","abstract":[{"lang":"eng","text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes."}],"department":[{"_id":"ToHe"}],"page":"24","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2010-0003","publication_status":"published","year":"2010","file":[{"file_id":"5547","content_type":"application/pdf","file_name":"IST-2010-0003_IST-2010-0003.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:42Z","relation":"main_file","date_created":"2018-12-12T11:54:25Z","checksum":"284ded99764e32a583a8ea83fcea254b","creator":"system","file_size":367246}],"publication_identifier":{"issn":["2664-1690"]},"title":"Simulation distances","_id":"5389"},{"date_created":"2018-12-12T11:39:03Z","date_updated":"2020-07-14T23:04:41Z","date_published":"2010-06-04T00:00:00Z","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël","last_name":"Fijalkow"}],"publisher":"IST Austria","ddc":["000"],"pubrep_id":"26","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages."}],"type":"technical_report","status":"public","day":"04","file_date_updated":"2020-07-14T12:46:43Z","alternative_title":["IST Austria Technical Report"],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"21","department":[{"_id":"KrCh"}],"publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:43Z","date_created":"2018-12-12T11:54:10Z","relation":"main_file","creator":"system","file_size":395662,"checksum":"283d3604d76dd4d5161585d4c8625fbe","content_type":"application/pdf","file_id":"5532","file_name":"IST-2010-0002_IST-2010-0002.pdf","access_level":"open_access"}],"year":"2010","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2010-0002","title":"Topological, automata-theoretic and logical characterization of finitary languages","_id":"5390","publication_identifier":{"issn":["2664-1690"]},"citation":{"ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>"},"oa":1},{"status":"public","type":"technical_report","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"later_version","id":"4390","status":"public"}]},"file_date_updated":"2020-07-14T12:46:43Z","day":"19","oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"27","ddc":["004"],"abstract":[{"text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable.","lang":"eng"}],"date_published":"2010-04-19T00:00:00Z","author":[{"last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","full_name":"Zufferey, Damien"},{"last_name":"Chaudhuri","first_name":"Swarat","full_name":"Chaudhuri, Swarat"},{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"}],"publisher":"IST Austria","date_updated":"2023-02-23T12:09:09Z","date_created":"2018-12-12T11:39:04Z","citation":{"short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2010-0001","year":"2010","file":[{"content_type":"application/pdf","file_id":"5505","file_name":"IST-2010-0001_IST-2010-0001.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:43Z","relation":"main_file","date_created":"2018-12-12T11:53:44Z","checksum":"986645caad7dd85a6a091488f6c646dc","creator":"system","file_size":372286}],"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"title":"Model checking of linearizability of concurrent list implementations","_id":"5391","page":"27","department":[{"_id":"ToHe"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"apa":"Juhás, G., Kazlov, I., &#38; Juhásová, A. (2010). Instance Deadlock: A Mystery behind Frozen Programs. In <i>Applications and Theory of Petri Nets</i> (pp. 1–17). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>","mla":"Juhás, Gabriel, et al. “Instance Deadlock: A Mystery behind Frozen Programs.” <i>Applications and Theory of Petri Nets</i>, Springer Berlin Heidelberg, 2010, pp. 1–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>.","ista":"Juhás G, Kazlov I, Juhásová A. 2010.Instance Deadlock: A Mystery behind Frozen Programs. In: Applications and Theory of Petri Nets. , 1–17.","short":"G. Juhás, I. Kazlov, A. Juhásová, in:, Applications and Theory of Petri Nets, Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, pp. 1–17.","ieee":"G. Juhás, I. Kazlov, and A. Juhásová, “Instance Deadlock: A Mystery behind Frozen Programs,” in <i>Applications and Theory of Petri Nets</i>, Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp. 1–17.","ama":"Juhás G, Kazlov I, Juhásová A. Instance Deadlock: A Mystery behind Frozen Programs. In: <i>Applications and Theory of Petri Nets</i>. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010:1-17. doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>","chicago":"Juhás, Gabriel, Igor Kazlov, and Ana Juhásová. “Instance Deadlock: A Mystery behind Frozen Programs.” In <i>Applications and Theory of Petri Nets</i>, 1–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>."},"publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["9783642136740","9783642136757"]},"title":"Instance Deadlock: A Mystery behind Frozen Programs","_id":"5940","article_processing_charge":"No","publication":"Applications and Theory of Petri Nets","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-13675-7_1","publication_status":"published","year":"2010","page":"1-17","user_id":"4A997E50-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"book_chapter","status":"public","oa_version":"None","place":"Berlin, Heidelberg","author":[{"last_name":"Juhás","first_name":"Gabriel","full_name":"Juhás, Gabriel"},{"id":"4A997E50-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","full_name":"Kazlov, Igor","last_name":"Kazlov"},{"first_name":"Ana","full_name":"Juhásová, Ana","last_name":"Juhásová"}],"publisher":"Springer Berlin Heidelberg","date_published":"2010-01-01T00:00:00Z","date_updated":"2022-04-01T13:45:24Z","date_created":"2019-02-08T09:33:41Z"},{"abstract":[{"text":"It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes.","lang":"eng"}],"oa_version":"None","publist_id":"7210","extern":"1","day":"01","status":"public","type":"journal_article","date_updated":"2021-01-12T08:05:28Z","intvolume":"        17","date_created":"2018-12-11T11:47:24Z","issue":"6","author":[{"last_name":"Meyer","full_name":"Meyer, Krista","first_name":"Krista"},{"first_name":"Shih","full_name":"Lin, Shih","last_name":"Lin"},{"orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"first_name":"Yuefeng","full_name":"Gao, Yuefeng","last_name":"Gao"},{"first_name":"Dylan","full_name":"Taatjes, Dylan","last_name":"Taatjes"}],"publisher":"Nature Publishing Group","date_published":"2010-06-01T00:00:00Z","publication":"Nature Structural and Molecular Biology","_id":"598","article_processing_charge":"No","title":"P53 activates transcription by directing structural shifts in Mediator","volume":17,"language":[{"iso":"eng"}],"doi":"10.1038/nsmb.1816","publication_status":"published","year":"2010","oa":1,"citation":{"chicago":"Meyer, Krista, Shih Lin, Carrie Bernecky, Yuefeng Gao, and Dylan Taatjes. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>.","ama":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. 2010;17(6):753-760. doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>","ieee":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, and D. Taatjes, “P53 activates transcription by directing structural shifts in Mediator,” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6. Nature Publishing Group, pp. 753–760, 2010.","short":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, D. Taatjes, Nature Structural and Molecular Biology 17 (2010) 753–760.","ista":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. 2010. P53 activates transcription by directing structural shifts in Mediator. Nature Structural and Molecular Biology. 17(6), 753–760.","mla":"Meyer, Krista, et al. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6, Nature Publishing Group, 2010, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>.","apa":"Meyer, K., Lin, S., Bernecky, C., Gao, Y., &#38; Taatjes, D. (2010). P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932482/","open_access":"1"}],"month":"06","page":"753 - 760"},{"type":"journal_article","status":"public","file_date_updated":"2020-07-14T12:47:20Z","extern":"1","day":"11","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by.png","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)"},"abstract":[{"text":"Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.","lang":"eng"}],"external_id":{"pmid":["21085631"]},"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2019-03-20T15:20:30Z","language":[{"iso":"eng"}],"year":"2010","publication_identifier":{"issn":["1932-6203"]},"volume":5,"pmid":1,"month":"11","oa_version":"Published Version","date_published":"2010-11-11T00:00:00Z","author":[{"first_name":"Katherine P.","full_name":"Weber, Katherine P.","last_name":"Weber"},{"full_name":"De, Subhajyoti","first_name":"Subhajyoti","last_name":"De"},{"last_name":"Kozarewa","full_name":"Kozarewa, Iwanka","first_name":"Iwanka"},{"last_name":"Turner","full_name":"Turner, Daniel J.","first_name":"Daniel J."},{"last_name":"Babu","full_name":"Babu, M. Madan","first_name":"M. Madan"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"de Bono, Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443"}],"issue":"11","date_updated":"2021-01-12T08:06:20Z","intvolume":"         5","article_number":"e13922","citation":{"mla":"Weber, Katherine P., et al. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>, vol. 5, no. 11, e13922, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>.","apa":"Weber, K. P., De, S., Kozarewa, I., Turner, D. J., Babu, M. M., &#38; de Bono, M. (2010). Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>","short":"K.P. Weber, S. De, I. Kozarewa, D.J. Turner, M.M. Babu, M. de Bono, PLoS ONE 5 (2010).","ista":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. 2010. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS ONE. 5(11), e13922.","chicago":"Weber, Katherine P., Subhajyoti De, Iwanka Kozarewa, Daniel J. Turner, M. Madan Babu, and Mario de Bono. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>.","ama":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. 2010;5(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>","ieee":"K. P. Weber, S. De, I. Kozarewa, D. J. Turner, M. M. Babu, and M. de Bono, “Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans,” <i>PLoS ONE</i>, vol. 5, no. 11. Public Library of Science, 2010."},"oa":1,"doi":"10.1371/journal.pone.0013922","file":[{"creator":"kschuh","file_size":578059,"checksum":"a01e6bbe15f044c0c79a26d7d881953e","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","date_created":"2019-03-20T15:22:48Z","access_level":"open_access","content_type":"application/pdf","file_id":"6143","file_name":"2010_PLOS_Weber.PDF"}],"publication_status":"published","publication":"PLoS ONE","_id":"6142","title":"Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"page":"173 - 179","month":"01","citation":{"short":"W. Zacharasiewicz, F. Kirsch, in:, Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien, Facultas.WUV, 2010, pp. 173–179.","ista":"Zacharasiewicz W, Kirsch F. 2010.“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien. , 173–179.","mla":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, Facultas.WUV, 2010, pp. 173–79.","apa":"Zacharasiewicz, W., &#38; Kirsch, F. (2010). “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i> (pp. 173–179). Facultas.WUV.","ieee":"W. Zacharasiewicz and F. Kirsch, “‘This is a fundamentalist town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House,” in <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i>, Facultas.WUV, 2010, pp. 173–179.","ama":"Zacharasiewicz W, Kirsch F. “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>. Facultas.WUV; 2010:173-179.","chicago":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” In <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, 173–79. Facultas.WUV, 2010."},"_id":"619","title":"“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House","publication":"Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien","year":"2010","publication_status":"published","quality_controlled":0,"publisher":"Facultas.WUV","author":[{"full_name":"Zacharasiewicz, Waldemar","first_name":"Waldemar","last_name":"Zacharasiewicz"},{"first_name":"Fritz","full_name":"Kirsch, Fritz Peter","last_name":"Kirsch"}],"date_published":"2010-01-01T00:00:00Z","date_updated":"2021-01-12T08:06:40Z","date_created":"2018-12-11T11:47:32Z","day":"01","extern":1,"type":"book_chapter","status":"public","abstract":[{"lang":"eng","text":"Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place."}],"publist_id":"7185"},{"date_updated":"2021-01-12T08:06:43Z","date_created":"2019-04-04T14:55:32Z","intvolume":"        16","issue":"12","external_id":{"pmid":["21102461"]},"author":[{"first_name":"L","full_name":"Zhou, L","last_name":"Zhou"},{"last_name":"Li","first_name":"F","full_name":"Li, F"},{"first_name":"Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Haibing","last_name":"Xu"},{"first_name":"CX","full_name":"Luo, CX","last_name":"Luo"},{"last_name":"Wu","full_name":"Wu, HY","first_name":"HY"},{"first_name":"MM","full_name":"Zhu, MM","last_name":"Zhu"},{"last_name":"Lu","first_name":"W","full_name":"Lu, W"},{"first_name":"X","full_name":"Ji, X","last_name":"Ji"},{"last_name":"Zhou","first_name":"QG","full_name":"Zhou, QG"},{"last_name":"Zhu","full_name":"Zhu, DY","first_name":"DY"}],"quality_controlled":"1","publisher":"Nature Publishing Group","date_published":"2010-11-21T00:00:00Z","abstract":[{"lang":"eng","text":"Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. "}],"oa_version":"None","day":"21","extern":"1","type":"journal_article","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"11","pmid":1,"page":"1439-1443","publication_identifier":{"issn":["1078-8956","1546-170x"]},"volume":16,"_id":"6198","title":"Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95","publication":"Nature Medicine","doi":"10.1038/nm.2245","language":[{"iso":"eng"}],"year":"2010","publication_status":"published","citation":{"chicago":"Zhou, L, F Li, Haibing Xu, CX Luo, HY Wu, MM Zhu, W Lu, X Ji, QG Zhou, and DY Zhu. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>.","ieee":"L. Zhou <i>et al.</i>, “Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95,” <i>Nature Medicine</i>, vol. 16, no. 12. Nature Publishing Group, pp. 1439–1443, 2010.","ama":"Zhou L, Li F, Xu H, et al. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. 2010;16(12):1439-1443. doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>","short":"L. Zhou, F. Li, H. Xu, C. Luo, H. Wu, M. Zhu, W. Lu, X. Ji, Q. Zhou, D. Zhu, Nature Medicine 16 (2010) 1439–1443.","ista":"Zhou L, Li F, Xu H, Luo C, Wu H, Zhu M, Lu W, Ji X, Zhou Q, Zhu D. 2010. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nature Medicine. 16(12), 1439–1443.","apa":"Zhou, L., Li, F., Xu, H., Luo, C., Wu, H., Zhu, M., … Zhu, D. (2010). Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>","mla":"Zhou, L., et al. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>, vol. 16, no. 12, Nature Publishing Group, 2010, pp. 1439–43, doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>."}}]