[{"citation":{"apa":"Kai, M., Buchan, N., Heisenberg, C.-P. J., &#38; Tada, M. (2009). Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>","ama":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S132-S132. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>","ieee":"M. Kai, N. Buchan, C.-P. J. Heisenberg, and M. Tada, “Regulation of planar cell polarity signalling by the prenylation pathway,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S132–S132, 2009.","ista":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. 2009. Regulation of planar cell polarity signalling by the prenylation pathway. Mechanisms of Development. 126(Supplement 1), S132–S132.","mla":"Kai, Masatake, et al. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S132–S132, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>.","chicago":"Kai, Masatake, Nina Buchan, Carl-Philipp J Heisenberg, and Masazumi Tada. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>.","short":"M. Kai, N. Buchan, C.-P.J. Heisenberg, M. Tada, Mechanisms of Development 126 (2009) S132–S132."},"publisher":"Elsevier","status":"public","year":"2009","doi":"10.1016/j.mod.2009.06.269","day":"05","publication_status":"published","month":"08","date_published":"2009-08-05T00:00:00Z","oa_version":"None","page":"S132 - S132","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"1927","publication":"Mechanisms of Development","date_created":"2018-12-11T12:07:30Z","intvolume":"       126","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, the body axis is established by a variety of co-ordinated and directed movements of cells. One of these movements is convergence and extension (CE), which is regulated by a non-canonical Wnt/planar cell polarity (PCP) pathway. From our forward genetic screen, we have identified 3-hydroxy-3-methyglutaryl-coenzyme A reductase 1b (hmgcr1b) gene as a dominant enhancer of the silberblick (slb)/wnt11 CE phenotype. hmgcr1b mutant embryos exhibit only very mild CE phenotype during gastrulation while showing a thicker yolk extension at pharyngula stages. Notably, abrogation of hmgcr1b also enhances the CE defects of other core PCP mutants/morphants. The prenylation pathway is one of branches downstream of HMGCR, and has been implicated for lipid modification at the C-terminus of proteins. To test the possibility that the prenylation pathway regulates activities of the PCP pathway, we abrogated farnesyl transferase (FT) or geranylgeranyl transferase (GGT) function using morpholinos on PCP mutant/morphant backgrounds. Consistent with the notion that FT preferentially performs lipid modification on to proteins with the CAAX motif including the core PCP protein Prickle (Pk), abrogation of FT, but not GGT, enhances the pk1a or pk1b morphant CE phenotype, suggesting the specif icity for targets of the prenylation enzymes.\r\n"}],"date_updated":"2021-01-12T07:55:11Z","type":"journal_article","volume":126,"_id":"4192","extern":"1","issue":"Supplement 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Regulation of planar cell polarity signalling by the prenylation pathway","author":[{"full_name":"Kai, Masatake","last_name":"Kai","first_name":"Masatake"},{"first_name":"Nina","last_name":"Buchan","full_name":"Buchan, Nina"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"first_name":"Masazumi","last_name":"Tada","full_name":"Tada, Masazumi"}]},{"doi":"10.1002/bies.200900109","day":"01","publication_status":"published","month":"12","date_published":"2009-12-01T00:00:00Z","page":"1284 - 1287","language":[{"iso":"eng"}],"oa_version":"None","article_processing_charge":"No","citation":{"ieee":"C.-P. J. Heisenberg, “Dorsal closure in Drosophila: cells cannot get out of the tight spot,” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12. Wiley-Blackwell, pp. 1284–1287, 2009.","apa":"Heisenberg, C.-P. J. (2009). Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>","ama":"Heisenberg C-PJ. Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. 2009;31(12):1284-1287. doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>","mla":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12, Wiley-Blackwell, 2009, pp. 1284–87, doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>.","short":"C.-P.J. Heisenberg, Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 31 (2009) 1284–1287.","chicago":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>.","ista":"Heisenberg C-PJ. 2009. Dorsal closure in Drosophila: cells cannot get out of the tight spot. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 31(12), 1284–1287."},"publisher":"Wiley-Blackwell","status":"public","year":"2009","_id":"4206","extern":"1","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dorsal closure in Drosophila: cells cannot get out of the tight spot","author":[{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"publist_id":"1911","publication":"Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology","date_created":"2018-12-11T12:07:35Z","intvolume":"        31","abstract":[{"lang":"eng","text":"Dorsal closure (DC), the closure of a hole in the dorsal epidermis of Drosophila embryos by the joining of opposing epithelial cell sheets, has been used as a model process to study the molecular and cellular mechanisms underlying epithelial spreading and wound healing. Recent studies have provided novel insights into how different tissues function cooperatively in this process. Specifically, they demonstrate a critical function of the epidermis surrounding the hole in modulating the behavior of the amnioserosa cells inside. These findings shed light not only on the mechanisms by which the behavior of different tissues is coordinated during DC, but also on the general mechanisms by which tissues interact to trigger global morphogenesis, an essential but yet poorly explored aspect of embryogenesis."}],"date_updated":"2021-01-12T07:55:17Z","type":"journal_article","volume":31},{"author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"first_name":"Jan","full_name":"Stuehmer, Jan","last_name":"Stuehmer"},{"full_name":"Bois, Justin","last_name":"Bois","first_name":"Justin"},{"first_name":"Yannis","full_name":"Kalaidzidis, Yannis","last_name":"Kalaidzidis"},{"last_name":"Lecaudey","full_name":"Lecaudey, Virginie","first_name":"Virginie"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Control of convergent yolk syncytial layer nuclear movement in zebrafish","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4217","extern":"1","issue":"8","type":"journal_article","date_updated":"2021-01-12T07:55:22Z","volume":136,"publication":"Development","date_created":"2018-12-11T12:07:39Z","publist_id":"1901","abstract":[{"lang":"eng","text":"Nuclear movements play an essential role in metazoan development. Although the intracellular transport mechanisms underlying nuclear movements have been studied in detail, relatively little is known about signals from surrounding cells and tissues controlling these movements. Here, we show that, in gastrulating zebrafish embryos, convergence movements of nuclei within the yolk syncytial layer (YSL) are guided by mesoderm and endoderm progenitors migrating along the surface of the yolk towards the dorsal side of the developing gastrula. Progenitor cells direct the convergence movements of internal yolk syncytial nuclei (iYSN) by modulating cortical flow within the YSL in which the iYSN are entrained. The effect of mesoderm and endoderm progenitors on the convergence movement of iYSN depends on the expression of E-cadherin, indicating that adhesive contact between the cells and the YSL is required for the mesendoderm-modulated YSL cortical flow mediating nuclear convergence. In summary, our data reveal a crucial function for cortical flow in the coordination of syncytial nuclear movements with surrounding cells and tissues during zebrafish gastrulation."}],"intvolume":"       136","page":"1305 - 1315","language":[{"iso":"eng"}],"oa_version":"None","article_processing_charge":"No","publication_status":"published","doi":"10.1242/dev.026922","day":"15","date_published":"2009-04-15T00:00:00Z","month":"04","year":"2009","citation":{"ieee":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, and C.-P. J. Heisenberg, “Control of convergent yolk syncytial layer nuclear movement in zebrafish,” <i>Development</i>, vol. 136, no. 8. Company of Biologists, pp. 1305–1315, 2009.","ama":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. 2009;136(8):1305-1315. doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>","apa":"Carvalho, L., Stuehmer, J., Bois, J., Kalaidzidis, Y., Lecaudey, V., &#38; Heisenberg, C.-P. J. (2009). Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>","mla":"Carvalho, Lara, et al. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>, vol. 136, no. 8, Company of Biologists, 2009, pp. 1305–15, doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>.","short":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, C.-P.J. Heisenberg, Development 136 (2009) 1305–1315.","chicago":"Carvalho, Lara, Jan Stuehmer, Justin Bois, Yannis Kalaidzidis, Virginie Lecaudey, and Carl-Philipp J Heisenberg. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>.","ista":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. 2009. Control of convergent yolk syncytial layer nuclear movement in zebrafish. Development. 136(8), 1305–1315."},"status":"public","publisher":"Company of Biologists"},{"article_processing_charge":"No","page":"875 - 883","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2009-08-18T00:00:00Z","month":"08","day":"18","doi":"10.1021/cb900151k","publication_status":"published","year":"2009","publisher":"American Chemical Society","main_file_link":[{"url":"10.1021/cb900151k [doi]"}],"status":"public","citation":{"chicago":"Swoboda, Jonathan, Timothy Meredith, Jennifer Campbell, Stephanie Brown, Takashi Suzuki, Mark Tobias Bollenbach, Amy Malhowski, Roy Kishony, Michael Gilmore, and Suzanne Walker. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>. American Chemical Society, 2009. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>.","short":"J. Swoboda, T. Meredith, J. Campbell, S. Brown, T. Suzuki, M.T. Bollenbach, A. Malhowski, R. Kishony, M. Gilmore, S. Walker, ACS Chemical Biology 4 (2009) 875–883.","mla":"Swoboda, Jonathan, et al. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>, vol. 4, no. 10, American Chemical Society, 2009, pp. 875–83, doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>.","ista":"Swoboda J, Meredith T, Campbell J, Brown S, Suzuki T, Bollenbach MT, Malhowski A, Kishony R, Gilmore M, Walker S. 2009. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. ACS Chemical Biology. 4(10), 875–883.","ieee":"J. Swoboda <i>et al.</i>, “Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus,” <i>ACS Chemical Biology</i>, vol. 4, no. 10. American Chemical Society, pp. 875–883, 2009.","apa":"Swoboda, J., Meredith, T., Campbell, J., Brown, S., Suzuki, T., Bollenbach, M. T., … Walker, S. (2009). Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>","ama":"Swoboda J, Meredith T, Campbell J, et al. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. 2009;4(10):875-883. doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>"},"author":[{"first_name":"Jonathan","last_name":"Swoboda","full_name":"Swoboda, Jonathan"},{"first_name":"Timothy","full_name":"Meredith, Timothy","last_name":"Meredith"},{"first_name":"Jennifer","full_name":"Campbell, Jennifer","last_name":"Campbell"},{"full_name":"Brown, Stephanie","last_name":"Brown","first_name":"Stephanie"},{"full_name":"Suzuki, Takashi","last_name":"Suzuki","first_name":"Takashi"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"},{"full_name":"Malhowski, Amy","last_name":"Malhowski","first_name":"Amy"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"},{"full_name":"Gilmore, Michael","last_name":"Gilmore","first_name":"Michael"},{"full_name":"Walker, Suzanne","last_name":"Walker","first_name":"Suzanne"}],"_id":"4223","issue":"10","extern":"1","title":"Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":4,"date_updated":"2021-01-12T07:55:25Z","type":"journal_article","intvolume":"         4","abstract":[{"text":"Both Gram-positive and Gram-negative bacteria contain bactoprenol-dependent biosynthetic pathways expressing non-essential cell surface polysaccharides that function as virulence factors. Although these polymers are not required for bacterial viability in vitro, genes in many of the biosynthetic pathways are conditionally essential: they cannot be deleted except in strains incapable of initiating polymer synthesis. We report a cell-based, pathway-specific strategy to screen for small molecule inhibitors of conditionally essential enzymes. The screen identifies molecules that prevent the growth of a wildtype bacterial strain but do not affect the growth of a mutant strain incapable of initiating polymer synthesis. We have applied this approach to discover inhibitors of wall teichoic acid (WTA) biosynthesis in Staphylococcus aureus. WTAs are anionic cell surface polysaccharides required for host colonization that have been suggested as targets for new antimicrobials. We have identified a small molecule, 7-chloro-N,N-diethyl-3-(phenylsulfonyl)-[1,2,3]triazolo[1,5-a]quinolin-5-amine (1835F03), that inhibits the growth of a panel of S. aureus strains (MIC = 1−3 μg mL−1), including clinical methicillin-resistant S. aureus (MRSA) isolates. Using a combination of biochemistry and genetics, we have identified the molecular target as TarG, the transmembrane component of the ABC transporter that exports WTAs to the cell surface. We also show that preventing the completion of WTA biosynthesis once it has been initiated triggers growth arrest. The discovery of 1835F03 validates our chemical genetics strategy for identifying inhibitors of conditionally essential enzymes, and the strategy should be applicable to many other bactoprenol-dependent biosynthetic pathways in the pursuit of novel antibacterials and probes of bacterial stress responses.","lang":"eng"}],"publist_id":"1894","publication":"ACS Chemical Biology","date_created":"2018-12-11T12:07:41Z"},{"title":"Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions","issue":"4","_id":"4228","extern":1,"author":[{"first_name":"Tobias","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"},{"full_name":"Quan, Selwyn","last_name":"Quan","first_name":"Selwyn"},{"first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Remy Chait","last_name":"Chait"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"publication":"Cell","date_created":"2018-12-11T12:07:43Z","publist_id":"1890","intvolume":"       139","abstract":[{"lang":"eng","text":"Suppressive drug interactions, in which one antibiotic can actually help bacterial cells to grow faster in the presence of another, occur between protein and DNA synthesis inhibitors. Here, we show that this suppression results from nonoptimal regulation of ribosomal genes in the presence of DNA stress. Using GFP-tagged transcription reporters in Escherichia coli, we find that ribosomal genes are not directly regulated by DNA stress, leading to an imbalance between cellular DNA and protein content. To test whether ribosomal gene expression under DNA stress is nonoptimal for growth rate, we sequentially deleted up to six of the seven ribosomal RNA operons. These synthetic manipulations of ribosomal gene expression correct the protein-DNA imbalance, lead to improved survival and growth, and completely remove the suppressive drug interaction. A simple mathematical model explains the nonoptimal regulation in different nutrient environments. These results reveal the genetic mechanism underlying an important class of suppressive drug interactions."}],"type":"journal_article","date_updated":"2021-01-12T07:55:27Z","volume":139,"publication_status":"published","doi":"10.1016/j.cell.2009.10.025","day":"01","month":"01","date_published":"2009-01-01T00:00:00Z","page":"707 - 718","quality_controlled":0,"citation":{"ieee":"T. Bollenbach, S. Quan, R. P. Chait, and R. Kishony, “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions,” <i>Cell</i>, vol. 139, no. 4. Cell Press, pp. 707–718, 2009.","apa":"Bollenbach, T., Quan, S., Chait, R. P., &#38; Kishony, R. (2009). Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>","ama":"Bollenbach T, Quan S, Chait RP, Kishony R. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. 2009;139(4):707-718. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>","short":"T. Bollenbach, S. Quan, R.P. Chait, R. Kishony, Cell 139 (2009) 707–718.","mla":"Bollenbach, Tobias, et al. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>, vol. 139, no. 4, Cell Press, 2009, pp. 707–18, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>.","chicago":"Bollenbach, Tobias, Selwyn Quan, Remy P Chait, and Roy Kishony. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>.","ista":"Bollenbach T, Quan S, Chait RP, Kishony R. 2009. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. Cell. 139(4), 707–718."},"status":"public","publisher":"Cell Press","year":"2009"},{"citation":{"ieee":"N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” <i>Genetics</i>, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.","apa":"Barton, N. H., &#38; De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>","ama":"Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. 2009;181(3):997-1011. doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>","chicago":"Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","mla":"Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>.","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011."},"status":"public","acknowledgement":"N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” ","scopus_import":"1","doi":"10.1534/genetics.108.099309","day":"01","publication_status":"published","department":[{"_id":"NiBa"}],"corr_author":"1","month":"03","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"None","publication":"Genetics","date_created":"2018-12-11T12:07:44Z","abstract":[{"lang":"eng","text":"The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ &gt; 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection."}],"date_updated":"2025-09-30T09:52:35Z","type":"journal_article","title":"Statistical mechanics and the evolution of polygenic quantitative traits","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Genetics Society of America","year":"2009","date_published":"2009-03-01T00:00:00Z","page":"997 - 1011","article_processing_charge":"No","publist_id":"1882","intvolume":"       181","volume":181,"issue":"3","_id":"4231","external_id":{"isi":["000270213500018"]},"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"De Vladar, Harold","last_name":"De Vladar","first_name":"Harold"}],"isi":1},{"date_updated":"2025-07-02T06:46:07Z","type":"dissertation","publist_id":"1883","date_created":"2018-12-11T12:07:44Z","author":[{"full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","orcid":"0000-0002-5985-7653","first_name":"Harold"}],"extern":"1","_id":"4232","title":"Stochasticity and Variability in the dynamics and genetics of populations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2009","publisher":"Faculty of mathematical and natural sciences, University of Groningen","status":"public","citation":{"ieee":"H. de Vladar, “Stochasticity and Variability in the dynamics and genetics of populations,” Faculty of mathematical and natural sciences, University of Groningen, 2009.","apa":"de Vladar, H. (2009). <i>Stochasticity and Variability in the dynamics and genetics of populations</i>. Faculty of mathematical and natural sciences, University of Groningen.","ama":"de Vladar H. Stochasticity and Variability in the dynamics and genetics of populations. 2009.","mla":"de Vladar, Harold. <i>Stochasticity and Variability in the Dynamics and Genetics of Populations</i>. Faculty of mathematical and natural sciences, University of Groningen, 2009.","short":"H. de Vladar, Stochasticity and Variability in the Dynamics and Genetics of Populations, Faculty of mathematical and natural sciences, University of Groningen, 2009.","chicago":"Vladar, Harold de. “Stochasticity and Variability in the Dynamics and Genetics of Populations.” Faculty of mathematical and natural sciences, University of Groningen, 2009.","ista":"de Vladar H. 2009. Stochasticity and Variability in the dynamics and genetics of populations. Faculty of mathematical and natural sciences, University of Groningen."},"article_processing_charge":"No","oa_version":"None","language":[{"iso":"eng"}],"month":"01","date_published":"2009-01-01T00:00:00Z","day":"01","publication_status":"published"},{"_id":"4242","external_id":{"isi":["000265145800006"]},"issue":"5","isi":1,"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"De Cara, Maria","last_name":"De Cara","first_name":"Maria"}],"publist_id":"1866","intvolume":"        63","volume":63,"date_published":"2009-05-01T00:00:00Z","page":"1171 - 1190","article_processing_charge":"No","ddc":["570"],"publisher":"Wiley","year":"2009","pubrep_id":"551","title":"The evolution of strong reproductive isolation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"has_accepted_license":"1","publication":"Evolution; International Journal of Organic Evolution","date_created":"2018-12-11T12:07:48Z","abstract":[{"text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.","lang":"eng"}],"type":"journal_article","date_updated":"2025-09-30T09:52:11Z","file_date_updated":"2020-07-14T12:46:25Z","publication_status":"published","department":[{"_id":"NiBa"}],"day":"01","doi":"10.1111/j.1558-5646.2009.00622.x","corr_author":"1","month":"05","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Submitted Version","citation":{"ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>.","apa":"Barton, N. H., &#38; De Cara, M. (2009). The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. 2009;63(5):1171-1190. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009."},"file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"1920d2e25ef335833764256c1a47bbfb","file_id":"4903","date_created":"2018-12-12T10:11:46Z","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","date_updated":"2020-07-14T12:46:25Z","file_size":720913,"creator":"system"},{"content_type":"application/pdf","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","creator":"system","file_size":290160,"file_id":"4904","date_created":"2018-12-12T10:11:47Z","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf"}],"status":"public","scopus_import":"1","acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio."},{"quality_controlled":0,"doi":"10.1103/PhysRevB.79.180511","day":"01","publication_status":"published","date_published":"2009-05-01T00:00:00Z","month":"05","acknowledgement":"This work was supported by ETH Zurich, the Swiss National Science Foundation, and by the EC via the EuroSQIP project and the Marie-Curie program (P. J. L.)","year":"2009","citation":{"ista":"Leek P, Filipp S, Maurer P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Wallraff A. 2009. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 79(18).","mla":"Leek, Peter, et al. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 79, no. 18, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">10.1103/PhysRevB.79.180511</a>.","chicago":"Leek, Peter, Stefan Filipp, Patrick Maurer, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, and Andreas Wallraff. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">https://doi.org/10.1103/PhysRevB.79.180511</a>.","short":"P. Leek, S. Filipp, P. Maurer, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, A. Wallraff, Physical Review B - Condensed Matter and Materials Physics 79 (2009).","ama":"Leek P, Filipp S, Maurer P, et al. Using sideband transitions for two-qubit operations in superconducting circuits. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2009;79(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">10.1103/PhysRevB.79.180511</a>","apa":"Leek, P., Filipp, S., Maurer, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Using sideband transitions for two-qubit operations in superconducting circuits. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.79.180511\">https://doi.org/10.1103/PhysRevB.79.180511</a>","ieee":"P. Leek <i>et al.</i>, “Using sideband transitions for two-qubit operations in superconducting circuits,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 79, no. 18. American Physical Society, 2009."},"publisher":"American Physical Society","main_file_link":[{"url":"http://arxiv.org/abs/0812.2678","open_access":"1"}],"status":"public","oa":1,"author":[{"last_name":"Leek","full_name":"Leek, Peter J","first_name":"Peter"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"last_name":"Maurer","full_name":"Maurer, Patrick","first_name":"Patrick"},{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"last_name":"Göppl","full_name":"Göppl, M","first_name":"M"},{"first_name":"L.","full_name":"Steffen, L. Kraig","last_name":"Steffen"},{"last_name":"Wallraff","full_name":"Wallraff, Andreas","first_name":"Andreas"}],"_id":"1766","issue":"18","extern":1,"title":"Using sideband transitions for two-qubit operations in superconducting circuits","date_updated":"2021-01-12T06:53:04Z","type":"journal_article","volume":79,"publist_id":"5354","date_created":"2018-12-11T11:53:54Z","publication":"Physical Review B - Condensed Matter and Materials Physics","intvolume":"        79","abstract":[{"lang":"eng","text":"We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation."}]},{"day":"19","doi":"10.1103/PhysRevLett.102.243602","publication_status":"published","date_published":"2009-06-19T00:00:00Z","month":"06","quality_controlled":0,"citation":{"ista":"Baur M, Filipp S, Bianchetti R, Fink JM, Göppl M, Steffen L, Leek P, Blais A, Wallraff A. 2009. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 102(24).","mla":"Baur, Matthias, et al. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” <i>Physical Review Letters</i>, vol. 102, no. 24, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">10.1103/PhysRevLett.102.243602</a>.","chicago":"Baur, Matthias, Stefan Filipp, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” <i>Physical Review Letters</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">https://doi.org/10.1103/PhysRevLett.102.243602</a>.","short":"M. Baur, S. Filipp, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 102 (2009).","ama":"Baur M, Filipp S, Bianchetti R, et al. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. <i>Physical Review Letters</i>. 2009;102(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">10.1103/PhysRevLett.102.243602</a>","apa":"Baur, M., Filipp, S., Bianchetti, R., Fink, J. M., Göppl, M., Steffen, L., … Wallraff, A. (2009). Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.102.243602\">https://doi.org/10.1103/PhysRevLett.102.243602</a>","ieee":"M. Baur <i>et al.</i>, “Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit,” <i>Physical Review Letters</i>, vol. 102, no. 24. American Physical Society, 2009."},"publisher":"American Physical Society","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/0812.4384","open_access":"1"}],"year":"2009","acknowledgement":"This work was supported by the Swiss National Science Foundation and by ETH Zürich. P. J. L. acknowledges support from the EC via an Intra-European Marie-Curie Fellowship. A. B. was supported by NSERC, CIFAR, FQRNT, and Alfred P. Sloan Foundation","_id":"1767","extern":1,"issue":"24","title":"Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit","oa":1,"author":[{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"},{"first_name":"R","full_name":"Bianchetti, R","last_name":"Bianchetti"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"first_name":"Peter","full_name":"Leek, Peter J","last_name":"Leek"},{"full_name":"Blais, Alexandre","last_name":"Blais","first_name":"Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"publist_id":"5352","date_created":"2018-12-11T11:53:54Z","publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives."}],"intvolume":"       102","date_updated":"2021-01-12T06:53:04Z","type":"journal_article","volume":102},{"author":[{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"},{"first_name":"Patrick","last_name":"Maurer","full_name":"Maurer, Patrick"},{"first_name":"Peter","full_name":"Leek, Peter J","last_name":"Leek"},{"last_name":"Baur","full_name":"Baur, Matthias P","first_name":"Matthias"},{"last_name":"Bianchetti","full_name":"Bianchetti, R","first_name":"R"},{"last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"L.","full_name":"Steffen, L. Kraig","last_name":"Steffen"},{"first_name":"Jay","last_name":"Gambetta","full_name":"Gambetta, Jay M"},{"full_name":"Blais, Alexandre","last_name":"Blais","first_name":"Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"oa":1,"_id":"1768","issue":"20","extern":1,"title":"Two-qubit state tomography using a joint dispersive readout","volume":102,"date_updated":"2021-01-12T06:53:04Z","type":"journal_article","intvolume":"       102","abstract":[{"lang":"eng","text":"Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states."}],"publist_id":"5353","date_created":"2018-12-11T11:53:54Z","publication":"Physical Review Letters","quality_controlled":0,"month":"05","date_published":"2009-05-18T00:00:00Z","doi":"10.1103/PhysRevLett.102.200402","day":"18","publication_status":"published","acknowledgement":"This work was supported by Swiss National Science Foundation (SNF) and ETH Zurich. P. J. L. was supported by the EC with a MC-EIF, J. M. G. by CIFAR, MRI, MITACS, and NSERC, and A. B. by NSERC and CIFAR","year":"2009","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.2485"}],"status":"public","citation":{"apa":"Filipp, S., Maurer, P., Leek, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Two-qubit state tomography using a joint dispersive readout. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.102.200402\">https://doi.org/10.1103/PhysRevLett.102.200402</a>","ama":"Filipp S, Maurer P, Leek P, et al. Two-qubit state tomography using a joint dispersive readout. <i>Physical Review Letters</i>. 2009;102(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.200402\">10.1103/PhysRevLett.102.200402</a>","ieee":"S. Filipp <i>et al.</i>, “Two-qubit state tomography using a joint dispersive readout,” <i>Physical Review Letters</i>, vol. 102, no. 20. American Physical Society, 2009.","ista":"Filipp S, Maurer P, Leek P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Gambetta J, Blais A, Wallraff A. 2009. Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. 102(20).","chicago":"Filipp, Stefan, Patrick Maurer, Peter Leek, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” <i>Physical Review Letters</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevLett.102.200402\">https://doi.org/10.1103/PhysRevLett.102.200402</a>.","mla":"Filipp, Stefan, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” <i>Physical Review Letters</i>, vol. 102, no. 20, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.102.200402\">10.1103/PhysRevLett.102.200402</a>.","short":"S. Filipp, P. Maurer, P. Leek, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, J. Gambetta, A. Blais, A. Wallraff, Physical Review Letters 102 (2009)."}},{"publication":"Physical Review Letters","date_created":"2018-12-11T11:53:55Z","publist_id":"5350","abstract":[{"text":"We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.","lang":"eng"}],"intvolume":"       103","type":"journal_article","date_updated":"2021-01-12T06:53:05Z","volume":103,"title":"Dressed collective qubit states and the Tavis-Cummings model in circuit QED","extern":1,"_id":"1769","issue":"8","oa":1,"author":[{"last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"first_name":"R","full_name":"Bianchetti, R","last_name":"Bianchetti"},{"last_name":"Baur","full_name":"Baur, Matthias P","first_name":"Matthias"},{"first_name":"M","full_name":"Göppl, M","last_name":"Göppl"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"full_name":"Filipp, Stefan","last_name":"Filipp","first_name":"Stefan"},{"last_name":"Leek","full_name":"Leek, Peter J","first_name":"Peter"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}],"citation":{"ista":"Fink JM, Bianchetti R, Baur M, Göppl M, Steffen L, Filipp S, Leek P, Blais A, Wallraff A. 2009. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. 103(8).","short":"J.M. Fink, R. Bianchetti, M. Baur, M. Göppl, L. Steffen, S. Filipp, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 103 (2009).","mla":"Fink, Johannes M., et al. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” <i>Physical Review Letters</i>, vol. 103, no. 8, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.103.083601\">10.1103/PhysRevLett.103.083601</a>.","chicago":"Fink, Johannes M, R Bianchetti, Matthias Baur, M Göppl, L. Steffen, Stefan Filipp, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” <i>Physical Review Letters</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevLett.103.083601\">https://doi.org/10.1103/PhysRevLett.103.083601</a>.","ama":"Fink JM, Bianchetti R, Baur M, et al. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. <i>Physical Review Letters</i>. 2009;103(8). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.103.083601\">10.1103/PhysRevLett.103.083601</a>","apa":"Fink, J. M., Bianchetti, R., Baur, M., Göppl, M., Steffen, L., Filipp, S., … Wallraff, A. (2009). Dressed collective qubit states and the Tavis-Cummings model in circuit QED. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.103.083601\">https://doi.org/10.1103/PhysRevLett.103.083601</a>","ieee":"J. M. Fink <i>et al.</i>, “Dressed collective qubit states and the Tavis-Cummings model in circuit QED,” <i>Physical Review Letters</i>, vol. 103, no. 8. American Physical Society, 2009."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.2651"}],"status":"public","publisher":"American Physical Society","acknowledgement":"This work was supported by SNF Grant No. 200021-111899 and ETHZ. P. J. L. was supported by the EU with a MC-EIF. A. B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation","year":"2009","publication_status":"published","doi":"10.1103/PhysRevLett.103.083601","day":"17","month":"08","date_published":"2009-08-17T00:00:00Z","quality_controlled":0},{"citation":{"short":"R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 80 (2009).","mla":"Bianchetti, R., et al. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 80, no. 4, American Physical Society, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevA.80.043840\">10.1103/PhysRevA.80.043840</a>.","chicago":"Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2009. <a href=\"https://doi.org/10.1103/PhysRevA.80.043840\">https://doi.org/10.1103/PhysRevA.80.043840</a>.","ista":"Bianchetti R, Filipp S, Baur M, Fink JM, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 80(4).","ieee":"R. Bianchetti <i>et al.</i>, “Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 80, no. 4. American Physical Society, 2009.","ama":"Bianchetti R, Filipp S, Baur M, et al. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2009;80(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.80.043840\">10.1103/PhysRevA.80.043840</a>","apa":"Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Göppl, M., Leek, P., … Wallraff, A. (2009). Dynamics of dispersive single-qubit readout 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.80.043840\">https://doi.org/10.1103/PhysRevA.80.043840</a>"},"publisher":"American Physical Society","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/0907.2549","open_access":"1"}],"year":"2009","acknowledgement":"This work was supported by the SNF Project No. 111899 and ETH Zurich. A.B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation","doi":"10.1103/PhysRevA.80.043840","day":"30","publication_status":"published","month":"10","date_published":"2009-10-30T00:00:00Z","quality_controlled":0,"publist_id":"5349","date_created":"2018-12-11T11:53:55Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","intvolume":"        80","abstract":[{"text":"The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.","lang":"eng"}],"date_updated":"2021-01-12T06:53:05Z","type":"journal_article","volume":80,"extern":1,"_id":"1770","issue":"4","title":"Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics","oa":1,"author":[{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"last_name":"Filipp","full_name":"Filipp, Stefan","first_name":"Stefan"},{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"last_name":"Leek","full_name":"Leek, Peter J","first_name":"Peter"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}]},{"publist_id":"5348","date_created":"2018-12-11T11:53:55Z","publication":"Physica Scripta T","abstract":[{"text":"The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits.","lang":"eng"}],"date_updated":"2021-01-12T06:53:06Z","type":"journal_article","volume":"T137","extern":1,"_id":"1771","title":"Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics","oa":1,"author":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"first_name":"Matthias","last_name":"Baur","full_name":"Baur, Matthias P"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"},{"last_name":"Göppl","full_name":"Göppl, M","first_name":"M"},{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"first_name":"Alexandre","full_name":"Blais, Alexandre","last_name":"Blais"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"citation":{"ista":"Fink JM, Baur M, Bianchetti R, Filipp S, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. T137.","chicago":"Fink, Johannes M, Matthias Baur, R Bianchetti, Stefan Filipp, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” <i>Physica Scripta T</i>. IOP Publishing Ltd., 2009. <a href=\"https://doi.org/10.1088/0031-8949/2009/T137/014013\">https://doi.org/10.1088/0031-8949/2009/T137/014013</a>.","short":"J.M. Fink, M. Baur, R. Bianchetti, S. Filipp, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physica Scripta T T137 (2009).","mla":"Fink, Johannes M., et al. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” <i>Physica Scripta T</i>, vol. T137, IOP Publishing Ltd., 2009, doi:<a href=\"https://doi.org/10.1088/0031-8949/2009/T137/014013\">10.1088/0031-8949/2009/T137/014013</a>.","apa":"Fink, J. M., Baur, M., Bianchetti, R., Filipp, S., Göppl, M., Leek, P., … Wallraff, A. (2009). Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. <i>Physica Scripta T</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0031-8949/2009/T137/014013\">https://doi.org/10.1088/0031-8949/2009/T137/014013</a>","ama":"Fink JM, Baur M, Bianchetti R, et al. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. <i>Physica Scripta T</i>. 2009;T137. doi:<a href=\"https://doi.org/10.1088/0031-8949/2009/T137/014013\">10.1088/0031-8949/2009/T137/014013</a>","ieee":"J. M. Fink <i>et al.</i>, “Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics,” <i>Physica Scripta T</i>, vol. T137. IOP Publishing Ltd., 2009."},"publisher":"IOP Publishing Ltd.","main_file_link":[{"url":"http://arxiv.org/abs/0911.3797","open_access":"1"}],"status":"public","acknowledgement":"Nobel Foundation","year":"2009","day":"01","doi":"10.1088/0031-8949/2009/T137/014013","publication_status":"published","date_published":"2009-01-01T00:00:00Z","month":"01","quality_controlled":0},{"year":"2009","publisher":"American Astronomical Society","article_processing_charge":"No","page":"547-559","date_published":"2009-01-15T00:00:00Z","volume":691,"intvolume":"       691","author":[{"first_name":"Sheng","full_name":"Wang, Sheng","last_name":"Wang"},{"first_name":"Zoltán","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"},{"first_name":"Morgan","last_name":"May","full_name":"May, Morgan"}],"issue":"1","_id":"17719","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/0004-637x/691/1/547"}],"status":"public","citation":{"chicago":"Wang, Sheng, Zoltán Haiman, and Morgan May. “Constraining Cosmology with High-Convergence Regions in Weak Lensing Surveys.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2009. <a href=\"https://doi.org/10.1088/0004-637x/691/1/547\">https://doi.org/10.1088/0004-637x/691/1/547</a>.","mla":"Wang, Sheng, et al. “Constraining Cosmology with High-Convergence Regions in Weak Lensing Surveys.” <i>The Astrophysical Journal</i>, vol. 691, no. 1, American Astronomical Society, 2009, pp. 547–59, doi:<a href=\"https://doi.org/10.1088/0004-637x/691/1/547\">10.1088/0004-637x/691/1/547</a>.","short":"S. Wang, Z. Haiman, M. May, The Astrophysical Journal 691 (2009) 547–559.","ista":"Wang S, Haiman Z, May M. 2009. Constraining cosmology with high-convergence regions in weak lensing surveys. The Astrophysical Journal. 691(1), 547–559.","ieee":"S. Wang, Z. Haiman, and M. May, “Constraining cosmology with high-convergence regions in weak lensing surveys,” <i>The Astrophysical Journal</i>, vol. 691, no. 1. American Astronomical Society, pp. 547–559, 2009.","apa":"Wang, S., Haiman, Z., &#38; May, M. (2009). Constraining cosmology with high-convergence regions in weak lensing surveys. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1088/0004-637x/691/1/547\">https://doi.org/10.1088/0004-637x/691/1/547</a>","ama":"Wang S, Haiman Z, May M. Constraining cosmology with high-convergence regions in weak lensing surveys. <i>The Astrophysical Journal</i>. 2009;691(1):547-559. doi:<a href=\"https://doi.org/10.1088/0004-637x/691/1/547\">10.1088/0004-637x/691/1/547</a>"},"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","month":"01","publication_status":"published","day":"15","doi":"10.1088/0004-637x/691/1/547","type":"journal_article","date_updated":"2024-09-25T13:44:05Z","abstract":[{"text":"We propose to use a simple observable, the fractional area of \"hot spots\" in weak gravitational lensing mass maps, which are detected with high significance, to determine background cosmological parameters. Because these high-convergence regions are directly related to the physical nonlinear structures of the universe, they derive cosmological information mainly from the nonlinear regime of density fluctuations. We show that in combination with future cosmic microwave background anisotropy measurements, this method can place constraints on cosmological parameters that are comparable to those from the redshift distribution of galaxy cluster abundances. The main advantage of the statistic proposed in this paper is that projection effects, normally the main source of uncertainty when determining the presence and the mass of a galaxy cluster, here serve as a source of information.","lang":"eng"}],"publication":"The Astrophysical Journal","date_created":"2024-09-06T09:03:38Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"oa":1,"article_type":"original","title":"Constraining cosmology with high-convergence regions in weak lensing surveys","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"year":"2009","publisher":"American Astronomical Society","article_processing_charge":"No","page":"1798-1822","date_published":"2009-05-10T00:00:00Z","volume":696,"intvolume":"       696","author":[{"full_name":"Tanaka, Takamitsu","last_name":"Tanaka","first_name":"Takamitsu"},{"last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán"}],"extern":"1","_id":"17735","issue":"2","scopus_import":"1","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/0004-637x/696/2/1798"}],"citation":{"ista":"Tanaka T, Haiman Z. 2009. The assembly of supermassive black holes at high redshifts. The Astrophysical Journal. 696(2), 1798–1822.","mla":"Tanaka, Takamitsu, and Zoltán Haiman. “The Assembly of Supermassive Black Holes at High Redshifts.” <i>The Astrophysical Journal</i>, vol. 696, no. 2, American Astronomical Society, 2009, pp. 1798–822, doi:<a href=\"https://doi.org/10.1088/0004-637x/696/2/1798\">10.1088/0004-637x/696/2/1798</a>.","short":"T. Tanaka, Z. Haiman, The Astrophysical Journal 696 (2009) 1798–1822.","chicago":"Tanaka, Takamitsu, and Zoltán Haiman. “The Assembly of Supermassive Black Holes at High Redshifts.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2009. <a href=\"https://doi.org/10.1088/0004-637x/696/2/1798\">https://doi.org/10.1088/0004-637x/696/2/1798</a>.","ama":"Tanaka T, Haiman Z. The assembly of supermassive black holes at high redshifts. <i>The Astrophysical Journal</i>. 2009;696(2):1798-1822. doi:<a href=\"https://doi.org/10.1088/0004-637x/696/2/1798\">10.1088/0004-637x/696/2/1798</a>","apa":"Tanaka, T., &#38; Haiman, Z. (2009). The assembly of supermassive black holes at high redshifts. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1088/0004-637x/696/2/1798\">https://doi.org/10.1088/0004-637x/696/2/1798</a>","ieee":"T. Tanaka and Z. Haiman, “The assembly of supermassive black holes at high redshifts,” <i>The Astrophysical Journal</i>, vol. 696, no. 2. American Astronomical Society, pp. 1798–1822, 2009."},"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"month":"05","day":"10","doi":"10.1088/0004-637x/696/2/1798","publication_status":"published","date_updated":"2024-09-26T13:45:27Z","type":"journal_article","abstract":[{"lang":"eng","text":"The supermassive black holes (SMBHs) massive enough to power the bright redshift ~6 quasars observed in the Sloan Digital Sky Survey (SDSS) are thought to have assembled by mergers and/or gas accretion from less massive \"seed\" BHs. If the seeds are the ~100 Msol remnant BHs from the first generation of stars, they must be in place well before redshift z=6, and must avoid being ejected from their parent proto-galaxies by the large (few hundred km/s) kicks they suffer from gravitational-radiation induced recoil during mergers with other BHs. We simulate the SMBH mass function at redshift z=6 using dark matter (DM) halo merger trees, coupled with a prescription for the halo occupation fraction, accretion histories, and radial recoil trajectories of the growing BHs. Our purpose is (i) to map out plausible scenarios for successful assembly of the z~6 quasar BHs by exploring a wide region of parameter space, and (ii) to predict the rate of low-frequency gravitational wave events detectable by the Laser Interferometer Space Antenna (LISA) for each such scenario. Our main findings are as follows: (1) ~100 Msol seed BHs can grow into the SDSS quasar BHs without super--Eddington accretion, but only if they form in minihalos by z~30 and subsequently accrete ~60% of the time; (2) the scenarios with optimistic assumptions required to explain the SDSS quasar BHs overproduce the mass density in lower--mass (10^5 to 10^7 Msol) SMBHs by a factor of 100-1000, unless seeds stop forming, or accrete at a severely diminished rates or duty cycles (e.g. due to feedback), at z < 20-30. We also present several successful assembly models and their LISA detection rates, including a \"maximal\" model that gives the highest rate (~30/yr at z~6) without overproducing the total SMBH density."}],"publication_identifier":{"issn":["0004-637X","1538-4357"]},"date_created":"2024-09-06T09:19:25Z","publication":"The Astrophysical Journal","oa":1,"article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The assembly of supermassive black holes at high redshifts"},{"volume":18,"intvolume":"        18","author":[{"first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman"}],"extern":"1","_id":"17736","year":"2009","publisher":"Cambridge University Press","article_processing_charge":"No","page":"157-173","date_published":"2009-08-17T00:00:00Z","editor":[{"first_name":"Mario","full_name":"Livio, Mario","last_name":"Livio"},{"first_name":"Stefano","full_name":"Casertano, Stefano","last_name":"Casertano"}],"date_updated":"2024-09-30T07:02:44Z","type":"book_chapter","abstract":[{"text":"We discuss currently available observational constraints on the reionization history of the intergalactic medium (IGM), and the extent to which accreting black holes (BHs) and stars can help account for these observations. We argue, based on the combined statistics of Lyman α and β absorption in quasar spectra, that the IGM contains a significant amount of neutral hydrogen with nH I/nH ≳ 0.1. On the other hand, we argue, based on the lack of a strong evolution in the observed abundance of Lyman α emitting galaxies beyond z ∼ 5.5, that the mean neutral hydrogen fraction cannot exceed nH I/nH ≈ 0.3 at the same redshift. We conclude that the IGM is experiencing rapid ionization at redshift z ∼ 6. We find that quasar BHs, including faint ones that are individually below the detection thresholds of existing optical and X-ray surveys, are unlikely to drive the evolution of the neutral fraction around this epoch, because they would over-produce the present-day soft X-ray background. On the other hand, the seeds of the z ∼ 6 quasar BHs likely appeared at much earlier epochs (z ∼ 20), and produced hard ionizing radiation by accretion. These early BHs are promising candidates to account for the high redshift (z ∼ 15) ionization implied by the recent cosmic microwave anisotropy data from WMAP. Using a model for the growth of BHs by accretion and mergers in a hierarchical cosmology, we suggest that the early growth of quasars must include a super-Eddington growth phase, and that, although not yet optically identified, the FIRST radio survey may have already detected several thousand > 10^8 M⊙ BHs at z > 6. ","lang":"eng"}],"series_title":" Space Telescope Science Institute Symposium Series","publication_identifier":{"isbn":["9780521847582"],"eisbn":["9780511536328"]},"date_created":"2024-09-06T09:20:03Z","publication":"Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope","conference":{"name":"Proceedings of the Space Telescope Science Institute Symposium","start_date":"2004-05-03","location":"Baltimore, MD, United States","end_date":"2004-05-06"},"place":"Baltimore","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Probing the reionization history of the Universe","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1017/CBO9780511536328.014"}],"status":"public","citation":{"ieee":"Z. Haiman, “Probing the reionization history of the Universe,” in <i>Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope</i>, vol. 18, M. Livio and S. Casertano, Eds. Baltimore: Cambridge University Press, 2009, pp. 157–173.","apa":"Haiman, Z. (2009). Probing the reionization history of the Universe. In M. Livio &#38; S. Casertano (Eds.), <i>Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope</i> (Vol. 18, pp. 157–173). Baltimore: Cambridge University Press. <a href=\"https://doi.org/10.1017/cbo9780511536328.014\">https://doi.org/10.1017/cbo9780511536328.014</a>","ama":"Haiman Z. Probing the reionization history of the Universe. In: Livio M, Casertano S, eds. <i>Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope</i>. Vol 18.  Space Telescope Science Institute Symposium Series. Baltimore: Cambridge University Press; 2009:157-173. doi:<a href=\"https://doi.org/10.1017/cbo9780511536328.014\">10.1017/cbo9780511536328.014</a>","mla":"Haiman, Zoltán. “Probing the Reionization History of the Universe.” <i>Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope</i>, edited by Mario Livio and Stefano Casertano, vol. 18, Cambridge University Press, 2009, pp. 157–73, doi:<a href=\"https://doi.org/10.1017/cbo9780511536328.014\">10.1017/cbo9780511536328.014</a>.","chicago":"Haiman, Zoltán. “Probing the Reionization History of the Universe.” In <i>Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope</i>, edited by Mario Livio and Stefano Casertano, 18:157–73.  Space Telescope Science Institute Symposium Series. Baltimore: Cambridge University Press, 2009. <a href=\"https://doi.org/10.1017/cbo9780511536328.014\">https://doi.org/10.1017/cbo9780511536328.014</a>.","short":"Z. Haiman, in:, M. Livio, S. Casertano (Eds.), Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope, Cambridge University Press, Baltimore, 2009, pp. 157–173.","ista":"Haiman Z. 2009.Probing the reionization history of the Universe. In: Planets to Cosmology. Essential Science in the Final Years of the Hubble Space Telescope. vol. 18, 157–173."},"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"None","month":"08","day":"17","doi":"10.1017/cbo9780511536328.014","publication_status":"published"},{"status":"public","main_file_link":[{"url":"https://doi.org/10.1088/0264-9381/26/9/094032","open_access":"1"}],"citation":{"ista":"Haiman Z, Kocsis B, Menou K, Lippai Z, Frei Z. 2009. Identifying decaying supermassive black hole binaries from their variable electromagnetic emission. Classical and Quantum Gravity. 26(9), 094032.","mla":"Haiman, Zoltán, et al. “Identifying Decaying Supermassive Black Hole Binaries from Their Variable Electromagnetic Emission.” <i>Classical and Quantum Gravity</i>, vol. 26, no. 9, 094032, IOP Publishing, 2009, doi:<a href=\"https://doi.org/10.1088/0264-9381/26/9/094032\">10.1088/0264-9381/26/9/094032</a>.","short":"Z. Haiman, B. Kocsis, K. Menou, Z. Lippai, Z. Frei, Classical and Quantum Gravity 26 (2009).","chicago":"Haiman, Zoltán, Bence Kocsis, Kristen Menou, Zoltán Lippai, and Zsolt Frei. “Identifying Decaying Supermassive Black Hole Binaries from Their Variable Electromagnetic Emission.” <i>Classical and Quantum Gravity</i>. IOP Publishing, 2009. <a href=\"https://doi.org/10.1088/0264-9381/26/9/094032\">https://doi.org/10.1088/0264-9381/26/9/094032</a>.","ama":"Haiman Z, Kocsis B, Menou K, Lippai Z, Frei Z. Identifying decaying supermassive black hole binaries from their variable electromagnetic emission. <i>Classical and Quantum Gravity</i>. 2009;26(9). doi:<a href=\"https://doi.org/10.1088/0264-9381/26/9/094032\">10.1088/0264-9381/26/9/094032</a>","apa":"Haiman, Z., Kocsis, B., Menou, K., Lippai, Z., &#38; Frei, Z. (2009). Identifying decaying supermassive black hole binaries from their variable electromagnetic emission. <i>Classical and Quantum Gravity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0264-9381/26/9/094032\">https://doi.org/10.1088/0264-9381/26/9/094032</a>","ieee":"Z. Haiman, B. Kocsis, K. Menou, Z. Lippai, and Z. Frei, “Identifying decaying supermassive black hole binaries from their variable electromagnetic emission,” <i>Classical and Quantum Gravity</i>, vol. 26, no. 9. IOP Publishing, 2009."},"scopus_import":"1","month":"05","publication_status":"published","day":"07","doi":"10.1088/0264-9381/26/9/094032","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"Supermassive black hole binaries (SMBHBs) with masses in the mass range ∼(10^4–10^7) M⊙/(1 + z), produced in galaxy mergers, are thought to complete their coalescence due to the emission of gravitational waves (GWs). The anticipated detection of the GWs by the future Laser Interferometric Space Antenna (LISA) will constitute a milestone for fundamental physics and astrophysics. While the GW signatures themselves will provide a treasure trove of information, if the source can be securely identified in electromagnetic (EM) bands, this would open up entirely new scientific opportunities, to probe fundamental physics, astrophysics and cosmology. We discuss several ideas, involving wide-field telescopes, that may be useful in locating electromagnetic counterparts to SMBHBs detected by LISA. In particular, the binary may produce a variable electromagnetic flux, such as a roughly periodic signal due to the orbital motion prior to coalescence, or a prompt transient signal caused by shocks in the circumbinary disc when the SMBHB recoils and 'shakes' the disc. We discuss whether these time-variable EM signatures may be detectable, and how they can help in identifying a unique counterpart within the localization errors provided by LISA. We also discuss a possibility of identifying a population of coalescing SMBHBs statistically, in a deep optical survey for periodically variable sources, before LISA detects the GWs directly. The discovery of such sources would confirm that gas is present in the vicinity and is being perturbed by the SMBHB—serving as a proof of concept for eventually finding actual LISA counterparts."}],"date_created":"2024-09-06T09:51:19Z","publication":"Classical and Quantum Gravity","publication_identifier":{"issn":["0264-9381","1361-6382"]},"type":"journal_article","date_updated":"2024-09-30T09:19:04Z","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Identifying decaying supermassive black hole binaries from their variable electromagnetic emission","oa":1,"publisher":"IOP Publishing","year":"2009","article_number":"094032","date_published":"2009-05-07T00:00:00Z","article_processing_charge":"No","intvolume":"        26","volume":26,"_id":"17764","issue":"9","extern":"1","author":[{"first_name":"Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán"},{"full_name":"Kocsis, Bence","last_name":"Kocsis","first_name":"Bence"},{"first_name":"Kristen","last_name":"Menou","full_name":"Menou, Kristen"},{"last_name":"Lippai","full_name":"Lippai, Zoltán","first_name":"Zoltán"},{"first_name":"Zsolt","full_name":"Frei, Zsolt","last_name":"Frei"}]},{"volume":400,"intvolume":"       400","author":[{"last_name":"Shang","full_name":"Shang, Cien","first_name":"Cien"},{"first_name":"Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán"},{"last_name":"Verde","full_name":"Verde, Licia","first_name":"Licia"}],"_id":"17765","issue":"2","extern":"1","year":"2009","publisher":"Oxford University Press","page":"1085-1104","article_processing_charge":"No","date_published":"2009-11-12T00:00:00Z","type":"journal_article","date_updated":"2024-09-30T09:24:18Z","date_created":"2024-09-06T09:51:57Z","publication":"Monthly Notices of the Royal Astronomical Society","publication_identifier":{"issn":["0035-8711","1365-2966"]},"abstract":[{"lang":"eng","text":"Scaling relations among galaxy cluster observables, which will become available in large future samples of galaxy clusters, could be used to constrain not only cluster structure, but also cosmology. We study the utility of this approach, employing a physically motivated parametric model to describe cluster structure and applying it to the expected relation between the Sunyaev–Zel'dovich decrement (Sν) and the emission-weighted X-ray temperature (Tew). The slope and normalization of the entropy profile, the concentration of the dark matter potential, the pressure at the virial radius and the level of non-thermal pressure support as well as the mass and redshift dependence of these quantities are described by free parameters. With a suitable choice of fiducial parameter values, the cluster model satisfies several existing observational constraints. We employ a Fisher matrix approach to estimate the joint errors on cosmological and cluster structure parameters from a measurement of Sν versus Tew in a future survey. We find that different cosmological parameters affect the scaling relation differently: predominantly through the baryon fraction (Ωm and Ωb), the virial overdensity (w0 and wa for low-z clusters) and the angular diameter distance (w0 and wa for high-z clusters; ΩDE and h). We find that the cosmology constraints from the scaling relation are comparable to those expected from the number counts (dN/dz) of the same clusters. The scaling-relation approach is relatively insensitive to selection effects and it offers a valuable consistency check; combining the information from the scaling relation and dN/dz is also useful to break parameter degeneracies and help disentangle cluster physics from cosmology. Our work suggests that scaling relations should be a useful component in extracting cosmological information from large future cluster surveys."}],"oa":1,"title":"Probing cosmology and galaxy cluster structure with the Sunyaev-Zel'dovich decrement versus X-ray temperature scaling relation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","scopus_import":"1","citation":{"ieee":"C. Shang, Z. Haiman, and L. Verde, “Probing cosmology and galaxy cluster structure with the Sunyaev-Zel’dovich decrement versus X-ray temperature scaling relation,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 400, no. 2. Oxford University Press, pp. 1085–1104, 2009.","apa":"Shang, C., Haiman, Z., &#38; Verde, L. (2009). Probing cosmology and galaxy cluster structure with the Sunyaev-Zel’dovich decrement versus X-ray temperature scaling relation. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/j.1365-2966.2009.15527.x\">https://doi.org/10.1111/j.1365-2966.2009.15527.x</a>","ama":"Shang C, Haiman Z, Verde L. Probing cosmology and galaxy cluster structure with the Sunyaev-Zel’dovich decrement versus X-ray temperature scaling relation. <i>Monthly Notices of the Royal Astronomical Society</i>. 2009;400(2):1085-1104. doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2009.15527.x\">10.1111/j.1365-2966.2009.15527.x</a>","mla":"Shang, Cien, et al. “Probing Cosmology and Galaxy Cluster Structure with the Sunyaev-Zel’dovich Decrement versus X-Ray Temperature Scaling Relation.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 400, no. 2, Oxford University Press, 2009, pp. 1085–104, doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2009.15527.x\">10.1111/j.1365-2966.2009.15527.x</a>.","chicago":"Shang, Cien, Zoltán Haiman, and Licia Verde. “Probing Cosmology and Galaxy Cluster Structure with the Sunyaev-Zel’dovich Decrement versus X-Ray Temperature Scaling Relation.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2009. <a href=\"https://doi.org/10.1111/j.1365-2966.2009.15527.x\">https://doi.org/10.1111/j.1365-2966.2009.15527.x</a>.","short":"C. Shang, Z. Haiman, L. Verde, Monthly Notices of the Royal Astronomical Society 400 (2009) 1085–1104.","ista":"Shang C, Haiman Z, Verde L. 2009. Probing cosmology and galaxy cluster structure with the Sunyaev-Zel’dovich decrement versus X-ray temperature scaling relation. Monthly Notices of the Royal Astronomical Society. 400(2), 1085–1104."},"main_file_link":[{"url":"https://doi.org/10.1111/j.1365-2966.2009.15527.x","open_access":"1"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","publication_status":"published","day":"12","doi":"10.1111/j.1365-2966.2009.15527.x","month":"11"},{"month":"12","day":"02","doi":"10.1111/j.1365-2966.2009.15552.x","publication_status":"published","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/j.1365-2966.2009.15552.x"}],"status":"public","citation":{"mla":"Kramer, R. H., and Zoltán Haiman. “Probing Re-Ionization with Quasar Spectra: The Impact of the Intrinsic Lyman α Emission Line Shape Uncertainty.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 400, no. 3, Oxford University Press, 2009, pp. 1493–511, doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2009.15552.x\">10.1111/j.1365-2966.2009.15552.x</a>.","chicago":"Kramer, R. H., and Zoltán Haiman. “Probing Re-Ionization with Quasar Spectra: The Impact of the Intrinsic Lyman α Emission Line Shape Uncertainty.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2009. <a href=\"https://doi.org/10.1111/j.1365-2966.2009.15552.x\">https://doi.org/10.1111/j.1365-2966.2009.15552.x</a>.","short":"R.H. Kramer, Z. Haiman, Monthly Notices of the Royal Astronomical Society 400 (2009) 1493–1511.","ista":"Kramer RH, Haiman Z. 2009. Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty. Monthly Notices of the Royal Astronomical Society. 400(3), 1493–1511.","ieee":"R. H. Kramer and Z. Haiman, “Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 400, no. 3. Oxford University Press, pp. 1493–1511, 2009.","ama":"Kramer RH, Haiman Z. Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty. <i>Monthly Notices of the Royal Astronomical Society</i>. 2009;400(3):1493-1511. doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2009.15552.x\">10.1111/j.1365-2966.2009.15552.x</a>","apa":"Kramer, R. H., &#38; Haiman, Z. (2009). Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/j.1365-2966.2009.15552.x\">https://doi.org/10.1111/j.1365-2966.2009.15552.x</a>"},"scopus_import":"1","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty","oa":1,"abstract":[{"lang":"eng","text":"Arguably the best hope of understanding the tail end of the re-ionization of the intergalactic medium (IGM) at redshift z > 6 is through the detection and characterization of the Gunn–Peterson damping wing absorption of the IGM in bright quasar spectra. However, the use of quasar spectra to measure the IGM damping wing requires a model of the quasar's intrinsic Lyman α emission line. Here we quantify the uncertainties in the intrinsic line shapes, and how those uncertainties affect the determination of the IGM neutral fraction. We have assembled a catalogue of high-resolution Hubble Space Telescope spectra of the emission lines of unobscured low-redshift quasars, and have characterized the variance in the shapes of their lines. We then add simulated absorption from the high-redshift IGM to these quasar spectra in order to determine the corresponding uncertainties in re-ionization constraints using current and future samples of z > 6 quasar spectra. We find that, if the redshift of the Lyman α emission line is presumed to coincide with the systemic redshift determined from metal lines, the inferred IGM neutral fraction is systematically biased to low values due to a systematic blueshift of the Lyman α line relative to the metal lines. If a similar blueshift persists in quasars at z > 6, this bias strengthens previous claims of a significant neutral hydrogen fraction at z≈ 6. The bias can be reduced by including a Lyman α blueshift in the modelling procedure, or by excising wavelengths near the Lyman α line centre from the modelling. Intrinsic Lyman α line shape variations still induce significant scatter in the inferred xIGM values. Nevertheless, this scatter still allows a robust distinction between a highly ionized (xIGM∼ 10−3) and a neutral (xIGM= 1) IGM with even a few bright quasars. We conclude that if the variations of the intrinsic Lyman α emission line shapes in high-z quasars are similar to those at low-z, this variation will not limit the usefulness of quasar spectra in probing re-ionization."}],"publication_identifier":{"issn":["0035-8711","1365-2966"]},"date_created":"2024-09-06T09:58:12Z","publication":"Monthly Notices of the Royal Astronomical Society","date_updated":"2024-09-30T09:48:06Z","type":"journal_article","date_published":"2009-12-02T00:00:00Z","article_processing_charge":"No","page":"1493-1511","publisher":"Oxford University Press","year":"2009","issue":"3","_id":"17769","extern":"1","author":[{"first_name":"R. H.","full_name":"Kramer, R. H.","last_name":"Kramer"},{"first_name":"Zoltán","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"}],"intvolume":"       400","volume":400}]