[{"intvolume":"       264","citation":{"mla":"Bozyigit, Deniz, et al. <i>Correlation Measurements of Individual Microwave Photons Emitted from a Symmetric Cavity</i>. Vol. 264, no. 1, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/1742-6596/264/1/012024\">10.1088/1742-6596/264/1/012024</a>.","ieee":"D. Bozyigit <i>et al.</i>, “Correlation measurements of individual microwave photons emitted from a symmetric cavity,” presented at the International Conference on Atomic Physics, 2011, vol. 264, no. 1.","chicago":"Bozyigit, Deniz, C Lang, L. Steffen, Johannes M Fink, Christopher Eichler, Matthias Baur, R Bianchetti, et al. “Correlation Measurements of Individual Microwave Photons Emitted from a Symmetric Cavity,” Vol. 264. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/1742-6596/264/1/012024\">https://doi.org/10.1088/1742-6596/264/1/012024</a>.","ista":"Bozyigit D, Lang C, Steffen L, Fink JM, Eichler C, Baur M, Bianchetti R, Leek P, Filipp S, Wallraff A, Da Silva M, Blais A. 2011. Correlation measurements of individual microwave photons emitted from a symmetric cavity. International Conference on Atomic Physics, Journal of Physics: Conference Series, vol. 264.","apa":"Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., Eichler, C., Baur, M., … Blais, A. (2011). Correlation measurements of individual microwave photons emitted from a symmetric cavity (Vol. 264). Presented at the International Conference on Atomic Physics, IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-6596/264/1/012024\">https://doi.org/10.1088/1742-6596/264/1/012024</a>","ama":"Bozyigit D, Lang C, Steffen L, et al. Correlation measurements of individual microwave photons emitted from a symmetric cavity. In: Vol 264. IOP Publishing Ltd.; 2011. doi:<a href=\"https://doi.org/10.1088/1742-6596/264/1/012024\">10.1088/1742-6596/264/1/012024</a>","short":"D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, C. Eichler, M. Baur, R. Bianchetti, P. Leek, S. Filipp, A. Wallraff, M. Da Silva, A. Blais, in:, IOP Publishing Ltd., 2011."},"day":"01","extern":1,"abstract":[{"lang":"eng","text":"Superconducting circuits have been successfully established as systems to prepare and investigate microwave light fields at the quantum level. In contrast to optical experiments where light is detected using photon counters, microwaves are usually measured with well developed linear amplifiers. This makes measurements of correlation functions - one of the important tools in optics - harder to achieve because they traditionally rely on photon counters and beam splitters. Here, we demonstrate a system where we can prepare on demand single microwave photons in a cavity and detect them at the two outputs of the cavity using linear amplifiers. Together with efficient data processing, this allows us to measure different observables of the cavity photons, including the first-order correlation function. Using these techniques we demonstrate cooling of a thermal background field in the cavity."}],"volume":264,"status":"public","date_updated":"2019-04-26T07:22:05Z","date_created":"2018-12-11T11:53:57Z","year":"2011","quality_controlled":0,"author":[{"last_name":"Bozyigit","first_name":"Deniz","full_name":"Bozyigit, Deniz"},{"last_name":"Lang","full_name":"Lang, C","first_name":"C"},{"last_name":"Steffen","first_name":"L.","full_name":"Steffen, L. Kraig"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Johannes Fink","last_name":"Fink"},{"full_name":"Eichler, Christopher","first_name":"Christopher","last_name":"Eichler"},{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"full_name":"Bianchetti, R","first_name":"R","last_name":"Bianchetti"},{"first_name":"Peter","full_name":"Leek, Peter J","last_name":"Leek"},{"last_name":"Filipp","first_name":"Stefan","full_name":"Filipp, Stefan"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"},{"first_name":"Marcus","full_name":"Da Silva, Marcus P","last_name":"Da Silva"},{"first_name":"Alexandre","full_name":"Blais, Alexandre","last_name":"Blais"}],"publist_id":"5339","issue":"1","alternative_title":["Journal of Physics: Conference Series"],"acknowledgement":"Australian National University,Aust. Res. Counc. Cent. Excellence Quantum-Atom Opt.,Griffith University,Ian Potter Foundation,International Union of Pure and Applied Physics","date_published":"2011-01-01T00:00:00Z","conference":{"name":"International Conference on Atomic Physics"},"type":"conference","publication_status":"published","title":"Correlation measurements of individual microwave photons emitted from a symmetric cavity","publisher":"IOP Publishing Ltd.","month":"01","_id":"1776","doi":"10.1088/1742-6596/264/1/012024"},{"acknowledgement":"This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ","date_published":"2011-06-01T00:00:00Z","oa_version":"None","author":[{"last_name":"Eichler","full_name":"Eichler, Christopher","first_name":"Christopher"},{"last_name":"Bozyigit","full_name":"Bozyigit, Deniz","first_name":"Deniz"},{"first_name":"C","full_name":"Lang, C","last_name":"Lang"},{"last_name":"Steffen","full_name":"Steffen, L.","first_name":"L."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"}],"publist_id":"5338","issue":"22","publication":"Physical Review Letters","publisher":"American Physical Society","month":"06","_id":"1777","doi":"10.1103/PhysRevLett.106.220503","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1103/PhysRevLett.106.249901","relation":"erratum"}]},"title":"Experimental state tomography of itinerant single microwave photons","oa":1,"article_processing_charge":"No","day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1011.6668"}],"citation":{"ama":"Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. Experimental state tomography of itinerant single microwave photons. <i>Physical Review Letters</i>. 2011;106(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.106.220503\">10.1103/PhysRevLett.106.220503</a>","short":"C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, A. Wallraff, Physical Review Letters 106 (2011).","mla":"Eichler, Christopher, et al. “Experimental State Tomography of Itinerant Single Microwave Photons.” <i>Physical Review Letters</i>, vol. 106, no. 22, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.106.220503\">10.1103/PhysRevLett.106.220503</a>.","ieee":"C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J. M. Fink, and A. Wallraff, “Experimental state tomography of itinerant single microwave photons,” <i>Physical Review Letters</i>, vol. 106, no. 22. American Physical Society, 2011.","chicago":"Eichler, Christopher, Deniz Bozyigit, C Lang, L. Steffen, Johannes M Fink, and Andreas Wallraff. “Experimental State Tomography of Itinerant Single Microwave Photons.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.106.220503\">https://doi.org/10.1103/PhysRevLett.106.220503</a>.","apa":"Eichler, C., Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., &#38; Wallraff, A. (2011). Experimental state tomography of itinerant single microwave photons. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.106.220503\">https://doi.org/10.1103/PhysRevLett.106.220503</a>","ista":"Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. 2011. Experimental state tomography of itinerant single microwave photons. Physical Review Letters. 106(22)."},"intvolume":"       106","date_updated":"2021-11-16T07:57:13Z","year":"2011","date_created":"2018-12-11T11:53:57Z","extern":"1","abstract":[{"lang":"eng","text":"A wide range of experiments studying microwave photons localized in superconducting cavities have made important contributions to our understanding of the quantum properties of radiation. Propagating microwave photons, however, have so far been studied much less intensely. Here we present measurements in which we reconstruct the quantum state of itinerant single photon Fock states and their superposition with the vacuum by analyzing moments of the measured amplitude distribution up to fourth order. Using linear amplifiers and quadrature amplitude detectors, we have developed efficient methods to separate the detected single photon signal from the noise added by the amplifier. From our measurement data we have also reconstructed the corresponding Wigner function."}],"volume":106,"status":"public"},{"date_published":"2011-06-15T00:00:00Z","acknowledgement":"This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. M. P. d. S. was supported by NSERC. A. B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation","publist_id":"5336","publication":"Physical Review Letters","issue":"24","author":[{"last_name":"Lang","first_name":"C","full_name":"Lang, C"},{"last_name":"Bozyigit","first_name":"Deniz","full_name":"Bozyigit, Deniz"},{"last_name":"Eichler","first_name":"Christopher","full_name":"Eichler, Christopher"},{"full_name":"Steffen, L. Kraig","first_name":"L.","last_name":"Steffen"},{"last_name":"Fink","first_name":"Johannes M","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abdumalikov, Abdufarrukh A","first_name":"Abdufarrukh","last_name":"Abdumalikov"},{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"full_name":"Da Silva, Marcus P","first_name":"Marcus","last_name":"Da Silva"},{"last_name":"Blais","first_name":"Alexandre","full_name":"Blais, Alexandre"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"month":"06","_id":"1778","doi":"10.1103/PhysRevLett.106.243601","publisher":"American Physical Society","oa":1,"title":"Observation of resonant photon blockade at microwave frequencies using correlation function measurements","publication_status":"published","type":"journal_article","day":"15","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1102.0461"}],"intvolume":"       106","citation":{"short":"C. Lang, D. Bozyigit, C. Eichler, L. Steffen, J.M. Fink, A. Abdumalikov, M. Baur, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Physical Review Letters 106 (2011).","ama":"Lang C, Bozyigit D, Eichler C, et al. Observation of resonant photon blockade at microwave frequencies using correlation function measurements. <i>Physical Review Letters</i>. 2011;106(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.106.243601\">10.1103/PhysRevLett.106.243601</a>","ista":"Lang C, Bozyigit D, Eichler C, Steffen L, Fink JM, Abdumalikov A, Baur M, Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Observation of resonant photon blockade at microwave frequencies using correlation function measurements. Physical Review Letters. 106(24).","apa":"Lang, C., Bozyigit, D., Eichler, C., Steffen, L., Fink, J. M., Abdumalikov, A., … Wallraff, A. (2011). Observation of resonant photon blockade at microwave frequencies using correlation function measurements. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.106.243601\">https://doi.org/10.1103/PhysRevLett.106.243601</a>","chicago":"Lang, C, Deniz Bozyigit, Christopher Eichler, L. Steffen, Johannes M Fink, Abdufarrukh Abdumalikov, Matthias Baur, et al. “Observation of Resonant Photon Blockade at Microwave Frequencies Using Correlation Function Measurements.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.106.243601\">https://doi.org/10.1103/PhysRevLett.106.243601</a>.","mla":"Lang, C., et al. “Observation of Resonant Photon Blockade at Microwave Frequencies Using Correlation Function Measurements.” <i>Physical Review Letters</i>, vol. 106, no. 24, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.106.243601\">10.1103/PhysRevLett.106.243601</a>.","ieee":"C. Lang <i>et al.</i>, “Observation of resonant photon blockade at microwave frequencies using correlation function measurements,” <i>Physical Review Letters</i>, vol. 106, no. 24. American Physical Society, 2011."},"quality_controlled":0,"year":"2011","date_created":"2018-12-11T11:53:57Z","date_updated":"2021-01-12T06:53:08Z","status":"public","volume":106,"abstract":[{"lang":"eng","text":"Creating a train of single photons and monitoring its propagation and interaction is challenging in most physical systems, as photons generally interact very weakly with other systems. However, when confining microwave frequency photons in a transmission line resonator, effective photon-photon interactions can be mediated by qubits embedded in the resonator. Here, we observe the phenomenon of photon blockade through second-order correlation function measurements. The experiments clearly demonstrate antibunching in a continuously pumped source of single microwave photons measured by using microwave beam splitters, linear amplifiers, and quadrature amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering in Mollow-triplet-like spectra."}],"extern":1},{"date_created":"2018-12-11T11:53:58Z","year":"2011","quality_controlled":0,"date_updated":"2021-01-12T06:53:09Z","status":"public","extern":1,"abstract":[{"lang":"eng","text":"Continuous variable entanglement between two modes of a radiation field is usually studied at optical frequencies. Here we demonstrate experiments that show the entanglement between microwave photons of different energy in a broadband squeezed beam. We use a Josephson parametric amplifier to generate the two-mode correlated state and detect all four quadrature components simultaneously in a two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional phase space histograms for all possible pairs of quadratures allows us to determine the full covariance matrix, which is in good agreement with the one expected for a two-mode squeezed state."}],"volume":107,"day":"06","citation":{"ista":"Eichler C, Bozyigit D, Lang C, Baur M, Steffen L, Fink JM, Filipp S, Wallraff A. 2011. Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. 107(11).","chicago":"Eichler, Christopher, Deniz Bozyigit, C Lang, Matthias Baur, L. Steffen, Johannes M Fink, Stefan Filipp, and Andreas Wallraff. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.113601\">https://doi.org/10.1103/PhysRevLett.107.113601</a>.","apa":"Eichler, C., Bozyigit, D., Lang, C., Baur, M., Steffen, L., Fink, J. M., … Wallraff, A. (2011). Observation of two-mode squeezing in the microwave frequency domain. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.113601\">https://doi.org/10.1103/PhysRevLett.107.113601</a>","mla":"Eichler, Christopher, et al. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” <i>Physical Review Letters</i>, vol. 107, no. 11, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.113601\">10.1103/PhysRevLett.107.113601</a>.","ieee":"C. Eichler <i>et al.</i>, “Observation of two-mode squeezing in the microwave frequency domain,” <i>Physical Review Letters</i>, vol. 107, no. 11. American Physical Society, 2011.","short":"C. Eichler, D. Bozyigit, C. Lang, M. Baur, L. Steffen, J.M. Fink, S. Filipp, A. Wallraff, Physical Review Letters 107 (2011).","ama":"Eichler C, Bozyigit D, Lang C, et al. Observation of two-mode squeezing in the microwave frequency domain. <i>Physical Review Letters</i>. 2011;107(11). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.113601\">10.1103/PhysRevLett.107.113601</a>"},"intvolume":"       107","doi":"10.1103/PhysRevLett.107.113601","_id":"1780","month":"09","publisher":"American Physical Society","publication_status":"published","title":"Observation of two-mode squeezing in the microwave frequency domain","type":"journal_article","acknowledgement":"This work was supported by the European Research Council (ERC) through a Starting grant and by ETHZ. S. F. acknowledges the Austrian Science Foundation (FWF) for support","date_published":"2011-09-06T00:00:00Z","publist_id":"5334","publication":"Physical Review Letters","issue":"11","author":[{"last_name":"Eichler","full_name":"Eichler, Christopher","first_name":"Christopher"},{"first_name":"Deniz","full_name":"Bozyigit, Deniz","last_name":"Bozyigit"},{"last_name":"Lang","full_name":"Lang, C","first_name":"C"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"first_name":"L.","full_name":"Steffen, L. Kraig","last_name":"Steffen"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Johannes Fink"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}]},{"issue":"6","publist_id":"5335","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","author":[{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"},{"last_name":"Göppl","full_name":"Göppl, M","first_name":"M"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Johannes Fink","first_name":"Johannes M"},{"last_name":"Baur","full_name":"Baur, Matthias P","first_name":"Matthias"},{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"last_name":"Steffen","full_name":"Steffen, L. Kraig","first_name":"L."},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"}],"date_published":"2011-06-22T00:00:00Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (SNF), the Austrian Science Foundation (FWF), and ETH Zurich","title":"Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics","publication_status":"published","type":"journal_article","doi":"10.1103/PhysRevA.83.063827","_id":"1781","month":"06","publisher":"American Physical Society","intvolume":"        83","citation":{"ista":"Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6).","chicago":"Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">https://doi.org/10.1103/PhysRevA.83.063827</a>.","apa":"Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L., &#38; Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">https://doi.org/10.1103/PhysRevA.83.063827</a>","mla":"Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">10.1103/PhysRevA.83.063827</a>.","ieee":"S. Filipp <i>et al.</i>, “Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 6. American Physical Society, 2011.","short":"S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011).","ama":"Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2011;83(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.063827\">10.1103/PhysRevA.83.063827</a>"},"day":"22","status":"public","volume":83,"abstract":[{"lang":"eng","text":"Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies."}],"extern":1,"quality_controlled":0,"date_created":"2018-12-11T11:53:58Z","year":"2011","date_updated":"2021-01-12T06:53:09Z"},{"date_published":"2011-04-02T00:00:00Z","publist_id":"5291","publication":"Mathematical Biosciences and Engineering","issue":"2","author":[{"last_name":"Friedlander","full_name":"Tamar Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brenner, Naama","first_name":"Naama","last_name":"Brenner"}],"doi":"10.3934/mbe.2011.8.515","_id":"1815","month":"04","publisher":"Arizona State University","oa":1,"title":"Adaptive response and enlargement of dynamic range","publication_status":"published","type":"journal_article","day":"02","citation":{"short":"T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011) 515–526.","ama":"Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range. <i>Mathematical Biosciences and Engineering</i>. 2011;8(2):515-526. doi:<a href=\"https://doi.org/10.3934/mbe.2011.8.515\">10.3934/mbe.2011.8.515</a>","apa":"Friedlander, T., &#38; Brenner, N. (2011). Adaptive response and enlargement of dynamic range. <i>Mathematical Biosciences and Engineering</i>. Arizona State University. <a href=\"https://doi.org/10.3934/mbe.2011.8.515\">https://doi.org/10.3934/mbe.2011.8.515</a>","ista":"Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 8(2), 515–526.","chicago":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>. Arizona State University, 2011. <a href=\"https://doi.org/10.3934/mbe.2011.8.515\">https://doi.org/10.3934/mbe.2011.8.515</a>.","mla":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2, Arizona State University, 2011, pp. 515–26, doi:<a href=\"https://doi.org/10.3934/mbe.2011.8.515\">10.3934/mbe.2011.8.515</a>.","ieee":"T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic range,” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2. Arizona State University, pp. 515–526, 2011."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1003.2791"}],"intvolume":"         8","page":"515 - 526","quality_controlled":0,"year":"2011","date_created":"2018-12-11T11:54:10Z","date_updated":"2021-01-12T06:53:23Z","status":"public","abstract":[{"lang":"eng","text":"Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems."}],"volume":8,"extern":1},{"date_updated":"2021-01-12T06:53:42Z","date_created":"2018-12-11T11:54:25Z","year":"2011","page":"97 - 101","quality_controlled":0,"extern":1,"volume":79,"abstract":[{"text":"The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J&gt;2, the proportion of parameter space affording this maximum is extremely small.","lang":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"day":"01","citation":{"ama":"Novak S. The number of equilibria in the diallelic Levene model with multiple demes. <i>Theoretical Population Biology</i>. 2011;79(3):97-101. doi:<a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">10.1016/j.tpb.2010.12.002</a>","short":"S. Novak, Theoretical Population Biology 79 (2011) 97–101.","mla":"Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” <i>Theoretical Population Biology</i>, vol. 79, no. 3, Academic Press, 2011, pp. 97–101, doi:<a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">10.1016/j.tpb.2010.12.002</a>.","ieee":"S. Novak, “The number of equilibria in the diallelic Levene model with multiple demes,” <i>Theoretical Population Biology</i>, vol. 79, no. 3. Academic Press, pp. 97–101, 2011.","chicago":"Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” <i>Theoretical Population Biology</i>. Academic Press, 2011. <a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">https://doi.org/10.1016/j.tpb.2010.12.002</a>.","ista":"Novak S. 2011. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 79(3), 97–101.","apa":"Novak, S. (2011). The number of equilibria in the diallelic Levene model with multiple demes. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2010.12.002\">https://doi.org/10.1016/j.tpb.2010.12.002</a>"},"intvolume":"        79","publisher":"Academic Press","month":"05","_id":"1863","doi":"10.1016/j.tpb.2010.12.002","type":"journal_article","publication_status":"published","title":"The number of equilibria in the diallelic Levene model with multiple demes","acknowledgement":"FWF 21305","date_published":"2011-05-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"last_name":"Novak","first_name":"Sebastian","full_name":"Sebastian Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5236","publication":"Theoretical Population Biology","issue":"3"},{"date_published":"2011-08-25T00:00:00Z","acknowledgement":"This work was funded by the Medical Research Council.","author":[{"last_name":"Efremov","first_name":"Rouslan","full_name":"Efremov, Rouslan G"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","first_name":"Leonid A","last_name":"Sazanov"}],"publist_id":"5110","issue":"7361","publication":"Nature","publisher":"Nature Publishing Group","_id":"1973","month":"08","doi":"10.1038/nature10330","type":"journal_article","title":"Structure of the membrane domain of respiratory complex i","publication_status":"published","day":"25","intvolume":"       476","citation":{"apa":"Efremov, R., &#38; Sazanov, L. A. (2011). Structure of the membrane domain of respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature10330\">https://doi.org/10.1038/nature10330</a>","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature10330\">https://doi.org/10.1038/nature10330</a>.","ista":"Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory complex i. Nature. 476(7361), 414–421.","ieee":"R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory complex i,” <i>Nature</i>, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421, 2011.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” <i>Nature</i>, vol. 476, no. 7361, Nature Publishing Group, 2011, pp. 414–21, doi:<a href=\"https://doi.org/10.1038/nature10330\">10.1038/nature10330</a>.","short":"R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421.","ama":"Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex i. <i>Nature</i>. 2011;476(7361):414-421. doi:<a href=\"https://doi.org/10.1038/nature10330\">10.1038/nature10330</a>"},"date_updated":"2021-01-12T06:54:26Z","page":"414 - 421","quality_controlled":0,"year":"2011","date_created":"2018-12-11T11:54:59Z","volume":476,"abstract":[{"lang":"eng","text":"Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements."}],"extern":1,"status":"public"},{"day":"01","citation":{"mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” <i>Current Opinion in Structural Biology</i>, vol. 21, no. 4, Elsevier, 2011, pp. 532–40, doi:<a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">10.1016/j.sbi.2011.07.002</a>.","ieee":"R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the cell?,” <i>Current Opinion in Structural Biology</i>, vol. 21, no. 4. Elsevier, pp. 532–540, 2011.","apa":"Efremov, R., &#38; Sazanov, L. A. (2011). Respiratory complex I: “steam engine” of the cell? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">https://doi.org/10.1016/j.sbi.2011.07.002</a>","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">https://doi.org/10.1016/j.sbi.2011.07.002</a>.","ista":"Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the cell? Current Opinion in Structural Biology. 21(4), 532–540.","ama":"Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell? <i>Current Opinion in Structural Biology</i>. 2011;21(4):532-540. doi:<a href=\"https://doi.org/10.1016/j.sbi.2011.07.002\">10.1016/j.sbi.2011.07.002</a>","short":"R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011) 532–540."},"intvolume":"        21","year":"2011","date_created":"2018-12-11T11:54:59Z","quality_controlled":0,"page":"532 - 540","date_updated":"2021-01-12T06:54:27Z","status":"public","extern":1,"volume":21,"abstract":[{"text":"Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine.","lang":"eng"}],"acknowledgement":"The work in authors’ laboratory was funded by the Medical Research Council.","date_published":"2011-08-01T00:00:00Z","publist_id":"5111","publication":"Current Opinion in Structural Biology","issue":"4","author":[{"last_name":"Efremov","full_name":"Efremov, Rouslan G","first_name":"Rouslan"},{"full_name":"Leonid Sazanov","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"month":"08","_id":"1974","doi":"10.1016/j.sbi.2011.07.002","publisher":"Elsevier","publication_status":"published","title":"Respiratory complex I: 'steam engine' of the cell?","type":"journal_article"},{"status":"public","volume":286,"abstract":[{"lang":"eng","text":"Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 &quot;core&quot; subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 &quot;supernumerary&quot; subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or &quot;accessory&quot; subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria."}],"extern":1,"quality_controlled":0,"page":"5023 - 5033","year":"2011","date_created":"2018-12-11T11:55:00Z","date_updated":"2021-01-12T06:54:27Z","citation":{"short":"C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of Biological Chemistry 286 (2011) 5023–5033.","ama":"Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. <i>Journal of Biological Chemistry</i>. 2011;286(7):5023-5033. doi:<a href=\"https://doi.org/10.1074/jbc.M110.194993\">10.1074/jbc.M110.194993</a>","chicago":"Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and Leonid A Sazanov. “Evolution of Respiratory Complex I &#38;quot;Supernumerary&#38;quot; Subunits Are Present in the α-Proteobacterial Enzyme.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.M110.194993\">https://doi.org/10.1074/jbc.M110.194993</a>.","apa":"Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., &#38; Sazanov, L. A. (2011). Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M110.194993\">https://doi.org/10.1074/jbc.M110.194993</a>","ista":"Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033.","ieee":"C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution of respiratory complex I &#38;quot;Supernumerary&#38;quot; subunits are present in the α-proteobacterial enzyme,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033, 2011.","mla":"Yip, Chui, et al. “Evolution of Respiratory Complex I &#38;quot;Supernumerary&#38;quot; Subunits Are Present in the α-Proteobacterial Enzyme.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 7, American Society for Biochemistry and Molecular Biology, 2011, pp. 5023–33, doi:<a href=\"https://doi.org/10.1074/jbc.M110.194993\">10.1074/jbc.M110.194993</a>."},"intvolume":"       286","day":"18","title":"Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme","publication_status":"published","type":"journal_article","month":"02","_id":"1975","doi":"10.1074/jbc.M110.194993","publisher":"American Society for Biochemistry and Molecular Biology","issue":"7","publication":"Journal of Biological Chemistry","publist_id":"5112","author":[{"first_name":"Chui","full_name":"Yip, Chui Y","last_name":"Yip"},{"full_name":"Harbour, Michael E","first_name":"Michael","last_name":"Harbour"},{"full_name":"Jayawardena, Kamburapola G","first_name":"Kamburapola","last_name":"Jayawardena"},{"last_name":"Fearnley","full_name":"Fearnley, Ian M","first_name":"Ian"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","first_name":"Leonid A","last_name":"Sazanov"}],"date_published":"2011-02-18T00:00:00Z","acknowledgement":"This work was supported by the Medical Research Council. "},{"author":[{"last_name":"Loose","first_name":"Martin","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"},{"full_name":"Fischer-Friedrich, Elisabeth","first_name":"Elisabeth","last_name":"Fischer Friedrich"},{"full_name":"Herold, Christoph","first_name":"Christoph","last_name":"Herold"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"last_name":"Schwille","full_name":"Schwille, Petra ","first_name":"Petra"}],"publication":"Nature Structural and Molecular Biology","publist_id":"5098","issue":"5","date_published":"2011-05-01T00:00:00Z","acknowledgement":"This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.).","type":"journal_article","title":"Min protein patterns emerge from rapid rebinding and membrane interaction of MinE","publication_status":"published","publisher":"Nature Publishing Group","doi":"10.1038/nsmb.2037","_id":"1985","month":"05","citation":{"mla":"Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>.","ieee":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min protein patterns emerge from rapid rebinding and membrane interaction of MinE,” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011.","ista":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 18(5), 577–583.","apa":"Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., &#38; Schwille, P. (2011). Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>","chicago":"Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse, and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>.","ama":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. 2011;18(5):577-583. doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>","short":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583."},"intvolume":"        18","day":"01","abstract":[{"lang":"eng","text":"\n\nIn Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation."}],"volume":18,"extern":1,"status":"public","date_updated":"2021-01-12T06:54:31Z","quality_controlled":0,"page":"577 - 583","date_created":"2018-12-11T11:55:03Z","year":"2011"},{"author":[{"full_name":"Martin Loose","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karsten","full_name":"Kruse, Karsten","last_name":"Kruse"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "}],"publication":"Annual Review of Biophysics","publist_id":"5097","issue":"1","date_published":"2011-06-09T00:00:00Z","type":"journal_article","publication_status":"published","title":"Protein self-organization: Lessons from the min system","publisher":"Annual Reviews","_id":"1986","doi":"10.1146/annurev-biophys-042910-155332","month":"06","intvolume":"        40","citation":{"short":"M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336.","ama":"Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. 2011;40(1):315-336. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>","ista":"Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.","chicago":"Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2011. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>.","apa":"Loose, M., Kruse, K., &#38; Schwille, P. (2011). Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>","ieee":"M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” <i>Annual Review of Biophysics</i>, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011.","mla":"Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>."},"day":"09","extern":1,"abstract":[{"text":"One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell.","lang":"eng"}],"volume":40,"status":"public","date_updated":"2021-01-12T06:54:31Z","year":"2011","date_created":"2018-12-11T11:55:04Z","quality_controlled":0,"page":"315 - 336"},{"volume":108,"date_updated":"2023-11-07T11:50:29Z","quality_controlled":"1","page":"3952-3957","date_created":"2023-09-06T12:54:36Z","year":"2011","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1012668108"}],"pmid":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.1012668108","author":[{"last_name":"Bachmann","first_name":"Annett","full_name":"Bachmann, Annett"},{"first_name":"Dirk","full_name":"Wildemann, Dirk","last_name":"Wildemann"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Fischer","first_name":"Gunter","full_name":"Fischer, Gunter"},{"last_name":"Kiefhaber","first_name":"Thomas","full_name":"Kiefhaber, Thomas"}],"publication":"PNAS","issue":"10","date_published":"2011-01-12T00:00:00Z","oa_version":"Published Version","external_id":{"pmid":["21325613"]},"abstract":[{"text":"Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.","lang":"eng"}],"extern":"1","status":"public","intvolume":"       108","citation":{"ieee":"A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber, “Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction,” <i>PNAS</i>, vol. 108, no. 10. Proceedings of the National Academy of Sciences, pp. 3952–3957, 2011.","mla":"Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>, vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57, doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>.","chicago":"Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer, and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition State of a Coupled Protein Folding and Binding Reaction.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>.","apa":"Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., &#38; Kiefhaber, T. (2011). Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1012668108\">https://doi.org/10.1073/pnas.1012668108</a>","ista":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. PNAS. 108(10), 3952–3957.","ama":"Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. <i>PNAS</i>. 2011;108(10):3952-3957. doi:<a href=\"https://doi.org/10.1073/pnas.1012668108\">10.1073/pnas.1012668108</a>","short":"A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS 108 (2011) 3952–3957."},"keyword":["Multidisciplinary"],"day":"12","article_type":"original","title":"Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14305","month":"01"},{"day":"01","main_file_link":[{"url":"http://arxiv.org/abs/0810.2076","open_access":"1"}],"citation":{"mla":"Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>, vol. 160, no. 2, Duke University Press, 2011, pp. 323–400, doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>.","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties,” <i>Duke Mathematical Journal</i>, vol. 160, no. 2. Duke University Press, pp. 323–400, 2011.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” <i>Duke Mathematical Journal</i>. Duke University Press, 2011. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400.","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2011). Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-1444258\">https://doi.org/10.1215/00127094-1444258</a>","ama":"Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties. <i>Duke Mathematical Journal</i>. 2011;160(2):323-400. doi:<a href=\"https://doi.org/10.1215/00127094-1444258\">10.1215/00127094-1444258</a>","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal 160 (2011) 323–400."},"intvolume":"       160","date_updated":"2021-01-12T06:50:56Z","page":"323 - 400","quality_controlled":0,"date_created":"2018-12-11T11:52:11Z","year":"2011","abstract":[{"lang":"eng","text":"We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq)."}],"volume":160,"extern":1,"status":"public","date_published":"2011-01-01T00:00:00Z","acknowledgement":"Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01.\nRodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by a Research Scholarship from the Clay Mathematical Institute.","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel","last_name":"Hausel"},{"full_name":"Letellier, Emmanuel","first_name":"Emmanuel","last_name":"Letellier"},{"full_name":"Rodríguez Villegas, Fernando","first_name":"Fernando","last_name":"Rodríguez Villegas"}],"publication":"Duke Mathematical Journal","publist_id":"5728","issue":"2","publisher":"Duke University Press","_id":"1467","doi":"10.1215/00127094-1444258","month":"01","type":"journal_article","oa":1,"title":"Arithmetic harmonic analysis on character and quiver varieties","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:IST-2011-0001","_id":"5387","month":"02","publisher":"IST Austria","title":"Energy and mean-payoff parity Markov decision processes","related_material":{"record":[{"id":"3345","status":"public","relation":"later_version"}]},"oa":1,"language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2020-07-14T12:46:41Z","type":"technical_report","oa_version":"Published Version","date_published":"2011-02-16T00:00:00Z","department":[{"_id":"KrCh"}],"alternative_title":["IST Austria Technical Report"],"pubrep_id":"23","ddc":["000","005"],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"page":"20","date_created":"2018-12-12T11:39:02Z","year":"2011","date_updated":"2023-02-23T11:23:11Z","status":"public","abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"file":[{"checksum":"824d6c70e6d3feb3e836b009e0b3cf73","relation":"main_file","creator":"system","file_size":329976,"file_name":"IST-2011-0001_IST-2011-0001.pdf","date_updated":"2020-07-14T12:46:41Z","access_level":"open_access","content_type":"application/pdf","file_id":"5458","date_created":"2018-12-12T11:52:57Z"}],"day":"16","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"citation":{"ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p."}},{"date_published":"2011-06-08T00:00:00Z","author":[{"orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","full_name":"Onur Hosten","first_name":"Onur"}],"publication":"Nature","publist_id":"7224","issue":"7350","publisher":"Nature Publishing Group","doi":"10.1038/474170a","_id":"580","month":"06","type":"journal_article","publication_status":"published","title":"Quantum physics: How to catch a wave","day":"08","citation":{"ama":"Hosten O. Quantum physics: How to catch a wave. <i>Nature</i>. 2011;474(7350):170-171. doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>","short":"O. Hosten, Nature 474 (2011) 170–171.","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>.","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” <i>Nature</i>, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>.","ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>"},"intvolume":"       474","date_updated":"2021-01-12T08:03:34Z","year":"2011","date_created":"2018-12-11T11:47:18Z","page":"170 - 171","quality_controlled":0,"extern":1,"volume":474,"status":"public"},{"type":"conference","publication_status":"published","title":"Methods towards achieving precise birefringent focusing","publisher":"OSA","_id":"585","month":"01","doi":"10.1364/CLEO_AT.2011.JThB130","author":[{"last_name":"Schmid","full_name":"Schmid, David","first_name":"David"},{"first_name":"Shiraz","full_name":"Hazrat, Shiraz","last_name":"Hazrat"},{"first_name":"Radhika","full_name":"Rangarajan, Radhika","last_name":"Rangarajan"},{"full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"last_name":"Quint","full_name":"Quint, Stephan","first_name":"Stephan"},{"first_name":"Paul","full_name":"Kwiat, Paul G","last_name":"Kwiat"}],"publist_id":"7220","alternative_title":["Optics InfoBase Conference Papers"],"date_published":"2011-01-01T00:00:00Z","conference":{"name":"QELS: Quantum Electronics and Laser Science"},"extern":1,"abstract":[{"lang":"eng","text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n"}],"status":"public","date_updated":"2021-01-12T08:03:44Z","year":"2011","date_created":"2018-12-11T11:47:20Z","quality_controlled":0,"citation":{"ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","mla":"Schmid, David, et al. <i>Methods towards Achieving Precise Birefringent Focusing</i>. OSA, 2011, doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>.","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., &#38; Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>.","ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, ."},"day":"01"},{"issue":"6","publication":"Physical Review Letters","publist_id":"7223","author":[{"last_name":"Vrijsen","full_name":"Vrijsen, Geert","first_name":"Geert"},{"last_name":"Hosten","first_name":"Onur","full_name":"Onur Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"full_name":"Lee, Jongmin","first_name":"Jongmin","last_name":"Lee"},{"last_name":"Bernon","full_name":"Bernon, Simon","first_name":"Simon"},{"full_name":"Kasevich, Mark A","first_name":"Mark","last_name":"Kasevich"}],"date_published":"2011-08-04T00:00:00Z","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","publication_status":"published","type":"journal_article","_id":"586","doi":"10.1103/PhysRevLett.107.063904","month":"08","publisher":"American Physical Society","citation":{"ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. 2011;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” <i>Physical Review Letters</i>, vol. 107, no. 6. American Physical Society, 2011.","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>, vol. 107, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>.","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>.","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., &#38; Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>","ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6)."},"intvolume":"       107","day":"04","status":"public","volume":107,"abstract":[{"text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research.","lang":"eng"}],"extern":1,"quality_controlled":0,"date_created":"2018-12-11T11:47:20Z","year":"2011","date_updated":"2021-01-12T08:05:05Z"},{"date_published":"2011-03-01T00:00:00Z","oa_version":"None","author":[{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"last_name":"Grob","first_name":"Patricia","full_name":"Grob, Patricia"},{"last_name":"Ebmeier","first_name":"Christopher","full_name":"Ebmeier, Christopher"},{"first_name":"Eva","full_name":"Nogales, Eva","last_name":"Nogales"},{"last_name":"Taatjes","full_name":"Taatjes, Dylan","first_name":"Dylan"}],"publist_id":"7209","issue":"3","publication":"PLoS Biology","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"597","doi":"10.1371/journal.pbio.1000603","month":"03","type":"journal_article","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","citation":{"ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” <i>PLoS Biology</i>, vol. 9, no. 3. Public Library of Science, 2011.","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>, vol. 9, no. 3, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>.","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., &#38; Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>","chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>.","ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. 2011;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011)."},"intvolume":"         9","date_updated":"2021-01-12T08:05:25Z","date_created":"2018-12-11T11:47:24Z","year":"2011","volume":9,"abstract":[{"text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.","lang":"eng"}],"extern":"1","status":"public"},{"date_published":"2011-12-20T00:00:00Z","external_id":{"pmid":["22135454"]},"oa_version":"Submitted Version","author":[{"full_name":"Milward, K.","first_name":"K.","last_name":"Milward"},{"last_name":"Busch","full_name":"Busch, K. E.","first_name":"K. E."},{"last_name":"Murphy","first_name":"R. J.","full_name":"Murphy, R. J."},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","full_name":"de Bono, Mario","first_name":"Mario"},{"last_name":"Olofsson","full_name":"Olofsson, B.","first_name":"B."}],"issue":"51","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1106134109","type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"date_updated":"2021-01-12T08:06:18Z","year":"2011","date_created":"2019-03-20T14:30:06Z","page":"20672-20677","quality_controlled":"1","volume":108,"_id":"6137","month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","oa":1,"day":"20","citation":{"ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(51):20672-20677. doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>","short":"K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings of the National Academy of Sciences 108 (2011) 20672–20677.","ieee":"K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011.","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>.","ista":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 108(51), 20672–20677.","apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., &#38; Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>","chicago":"Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>."},"intvolume":"       108","extern":"1","abstract":[{"text":"Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies.","lang":"eng"}],"status":"public"}]