[{"file_date_updated":"2021-07-22T08:06:34Z","publication":"Journal of Structural Biology","abstract":[{"lang":"eng","text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells."}],"volume":186,"title":"Correlative light- and electron microscopy with chemical tags","external_id":{"pmid":["24698954"]},"article_processing_charge":"No","page":"205-213","date_created":"2021-07-14T09:05:42Z","doi":"10.1016/j.jsb.2014.03.018","publication_identifier":{"issn":["1047-8477"]},"_id":"9655","scopus_import":"1","citation":{"chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>.","ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. 2014;186(2):205-213. doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>","ieee":"M. Perkovic <i>et al.</i>, “Correlative light- and electron microscopy with chemical tags,” <i>Journal of Structural Biology</i>, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>.","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213."},"month":"05","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","issue":"2","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","ddc":["570"],"date_published":"2014-05-01T00:00:00Z","author":[{"first_name":"Mario","last_name":"Perkovic","full_name":"Perkovic, Mario"},{"full_name":"Kunz, Michael","last_name":"Kunz","first_name":"Michael"},{"first_name":"Ulrike","last_name":"Endesfelder","full_name":"Endesfelder, Ulrike"},{"full_name":"Bunse, Stefanie","last_name":"Bunse","first_name":"Stefanie"},{"full_name":"Wigge, Christoph","last_name":"Wigge","first_name":"Christoph"},{"first_name":"Zhou","last_name":"Yu","full_name":"Yu, Zhou"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Scheffer, Margot P.","last_name":"Scheffer","first_name":"Margot P."},{"full_name":"Seybert, Anja","last_name":"Seybert","first_name":"Anja"},{"first_name":"Sebastian","last_name":"Malkusch","full_name":"Malkusch, Sebastian"},{"first_name":"Erin M.","last_name":"Schuman","full_name":"Schuman, Erin M."},{"last_name":"Heilemann","first_name":"Mike","full_name":"Heilemann, Mike"},{"last_name":"Frangakis","first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)"},"extern":"1","intvolume":"       186","has_accepted_license":"1","status":"public","pmid":1,"publication_status":"published","publisher":"Elsevier","article_type":"original","date_updated":"2021-07-22T08:26:32Z","day":"01","year":"2014","file":[{"creator":"asandaue","file_size":3454628,"date_updated":"2021-07-22T08:06:34Z","content_type":"application/pdf","relation":"main_file","checksum":"a322991b43cdc5935c99db88d285aa3a","date_created":"2021-07-22T08:06:34Z","access_level":"open_access","success":1,"file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","file_id":"9701"}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/"},{"scopus_import":"1","citation":{"ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","apa":"Cheng, B., &#38; Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>.","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24. AIP Publishing, 2014.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>.","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. 2014;141(24). doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","type":"journal_article","doi":"10.1063/1.4904293","date_created":"2021-07-15T09:22:49Z","_id":"9662","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"main_file_link":[{"url":"https://arxiv.org/abs/1412.1308","open_access":"1"}],"oa":1,"oa_version":"Preprint","issue":"24","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Direct path integral estimators for isotope fractionation ratios","article_number":"244112","publication":"The Journal of Chemical Physics","abstract":[{"lang":"eng","text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons."}],"volume":141,"external_id":{"pmid":["25554138"],"arxiv":["1412.1308"]},"article_processing_charge":"No","arxiv":1,"article_type":"original","publisher":"AIP Publishing","date_updated":"2021-08-09T12:32:24Z","status":"public","publication_status":"published","pmid":1,"day":"28","year":"2014","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"date_published":"2014-12-28T00:00:00Z","extern":"1","intvolume":"       141"},{"abstract":[{"text":"It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings.","lang":"eng"}],"publication":"Philosophical Magazine","volume":95,"date_published":"2014-06-23T00:00:00Z","title":"Strength of metals under vibrations – dislocation-density-function dynamics simulations","author":[{"last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"full_name":"Leung, H.S.","last_name":"Leung","first_name":"H.S."},{"first_name":"A.H.W.","last_name":"Ngan","full_name":"Ngan, A.H.W."}],"intvolume":"        95","extern":"1","article_processing_charge":"No","page":"1845-1865","status":"public","date_created":"2021-07-19T09:27:15Z","doi":"10.1080/14786435.2014.897008","publication_identifier":{"eissn":["1478-6443"],"issn":["1478-6435"]},"_id":"9686","publication_status":"published","date_updated":"2023-02-23T14:04:59Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"06","type":"journal_article","scopus_import":"1","citation":{"chicago":"Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>.","ama":"Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. 2014;95(16-18):1845-1865. doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>","ieee":"B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” <i>Philosophical Magazine</i>, vol. 95, no. 16–18. Taylor &#38; Francis, pp. 1845–1865, 2014.","mla":"Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>, vol. 95, no. 16–18, Taylor &#38; Francis, 2014, pp. 1845–65, doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>.","short":"B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.","apa":"Cheng, B., Leung, H. S., &#38; Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>","ista":"Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865."},"publisher":"Taylor & Francis","article_type":"original","year":"2014","day":"23","issue":"16-18","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"None"},{"volume":112,"abstract":[{"text":"The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).","lang":"eng"}],"publication":"APS Physics, Physical Review Letters","article_number":"216806","title":"Antilocalization of coulomb blockade in a Ge/Si nanowire","arxiv":1,"external_id":{"arxiv":["1401.2948"]},"_id":"97","date_created":"2018-12-11T11:44:36Z","doi":"10.1103/PhysRevLett.112.216806","acknowledgement":"Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program.","main_file_link":[{"url":"https://arxiv.org/abs/1401.2948","open_access":"1"}],"citation":{"short":"A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","ieee":"A. P. Higginbotham <i>et al.</i>, “Antilocalization of coulomb blockade in a Ge/Si nanowire,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21. American Physical Society, 2014.","mla":"Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>.","ama":"Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. 2014;112(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>.","ista":"Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806.","apa":"Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>"},"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"21","oa_version":"None","oa":1,"date_published":"2014-05-29T00:00:00Z","publist_id":"7957","author":[{"first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"},{"first_name":"Thorvald","last_name":"Larsen","full_name":"Larsen, Thorvald"},{"full_name":"Fitzpatrick, Mattias","last_name":"Fitzpatrick","first_name":"Mattias"},{"full_name":"Yao, Jun","last_name":"Yao","first_name":"Jun"},{"full_name":"Yan, Hao","last_name":"Yan","first_name":"Hao"},{"first_name":"Charles","last_name":"Lieber","full_name":"Lieber, Charles"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"}],"extern":"1","intvolume":"       112","publication_status":"published","status":"public","publisher":"American Physical Society","date_updated":"2021-01-12T08:22:19Z","day":"29","year":"2014"},{"author":[{"last_name":"Lovrics","first_name":"Anna","full_name":"Lovrics, Anna"},{"first_name":"Yu","last_name":"Gao","full_name":"Gao, Yu"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"full_name":"Bock, István","last_name":"Bock","first_name":"István"},{"first_name":"Helen M.","last_name":"Byrne","full_name":"Byrne, Helen M."},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"first_name":"Krisztián","last_name":"Kovács","full_name":"Kovács, Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","date_published":"2014-11-14T00:00:00Z","article_processing_charge":"No","citation":{"ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>."},"publisher":"Public Library of Science","type":"research_data_reference","date_updated":"2025-09-29T12:02:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"11","_id":"9722","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2004"}]},"status":"public","doi":"10.1371/journal.pone.0111430.s006","date_created":"2021-07-26T14:35:00Z","department":[{"_id":"JoCs"}],"oa_version":"Published Version","day":"14","year":"2014"},{"article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"last_name":"Adlam","first_name":"Ben","full_name":"Adlam, Ben"},{"full_name":"Novak, Martin","last_name":"Novak","first_name":"Martin"}],"title":"Detailed proofs for “The time scale of evolutionary innovation”","date_published":"2014-09-11T00:00:00Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","day":"11","year":"2014","citation":{"apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014)."},"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2025-09-29T11:53:46Z","month":"09","type":"research_data_reference","status":"public","doi":"10.1371/journal.pcbi.1003818.s001","date_created":"2021-07-28T08:13:57Z","related_material":{"record":[{"id":"2039","relation":"used_in_publication","status":"public"}]},"_id":"9739"},{"oa":1,"oa_version":"Published Version","department":[{"_id":"SyCr"}],"year":"2014","day":"13","type":"research_data_reference","date_updated":"2025-09-23T07:55:02Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"11","publisher":"Dryad","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.vm0vc","open_access":"1"}],"_id":"9740","related_material":{"record":[{"id":"1993","relation":"used_in_publication","status":"public"}]},"date_created":"2021-07-28T08:38:40Z","status":"public","doi":"10.5061/dryad.vm0vc","article_processing_charge":"No","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V"},{"full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"corr_author":"1","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"date_published":"2014-11-13T00:00:00Z"},{"year":"2014","day":"21","oa":1,"oa_version":"Published Version","department":[{"_id":"CaGu"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"status":"public","date_created":"2021-07-28T08:48:06Z","doi":"10.5061/dryad.85dn7","_id":"9741","related_material":{"record":[{"id":"2036","relation":"used_in_publication","status":"public"}]},"date_updated":"2025-09-29T11:54:45Z","month":"08","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","citation":{"apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014."},"publisher":"Dryad","article_processing_charge":"No","abstract":[{"text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.","lang":"eng"}],"date_published":"2014-08-21T00:00:00Z","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","author":[{"first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"04","date_updated":"2025-09-29T11:46:47Z","type":"research_data_reference","citation":{"ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>"},"publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"doi":"10.5061/dryad.s42n1","date_created":"2021-07-28T15:32:55Z","status":"public","related_material":{"record":[{"id":"2083","status":"public","relation":"used_in_publication"}]},"_id":"9747","oa":1,"oa_version":"Published Version","department":[{"_id":"CaGu"}],"year":"2014","day":"17","title":"Data from: Role of sex and migration in adaptation to sink environments","author":[{"first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"}],"abstract":[{"lang":"eng","text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment."}],"date_published":"2014-04-17T00:00:00Z","article_processing_charge":"No"},{"related_material":{"record":[{"id":"2277","status":"public","relation":"used_in_publication"}]},"_id":"9752","doi":"10.5061/dryad.246qg","status":"public","date_created":"2021-07-30T08:13:52Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.246qg","open_access":"1"}],"citation":{"ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>."},"publisher":"Dryad","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2025-09-29T14:27:23Z","month":"11","day":"07","year":"2014","department":[{"_id":"GaTk"}],"oa_version":"Published Version","oa":1,"date_published":"2014-11-07T00:00:00Z","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"author":[{"full_name":"Simmons, Kristina","last_name":"Simmons","first_name":"Kristina"},{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"},{"full_name":"Homann, Jan","first_name":"Jan","last_name":"Homann"},{"first_name":"Heather","last_name":"Yee","full_name":"Yee, Heather"},{"full_name":"Palmer, Stephanie","last_name":"Palmer","first_name":"Stephanie"},{"full_name":"Nelson, Philip","first_name":"Philip","last_name":"Nelson"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"}],"title":"Data from: Transformation of stimulus correlations by the retina","article_processing_charge":"No"},{"date_published":"2014-10-08T00:00:00Z","abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}],"author":[{"first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"first_name":"Michel","last_name":"Chapuisat","full_name":"Chapuisat, Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2284"}]},"_id":"9753","status":"public","doi":"10.5061/dryad.nc0gc","date_created":"2021-07-30T08:24:11Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"citation":{"ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>","mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>"},"publisher":"Dryad","type":"research_data_reference","month":"10","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2025-09-29T14:24:12Z","day":"08","year":"2014","department":[{"_id":"SyCr"}],"oa_version":"Published Version","oa":1},{"type":"journal_article","month":"10","date_updated":"2021-01-12T08:22:22Z","citation":{"chicago":"Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>.","ama":"Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. <i>Physical Review Letters</i>. 2014;113(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>","ieee":"M. Serbyn <i>et al.</i>, “Interferometric probes of many-body localization,” <i>Physical Review Letters</i>, vol. 113, no. 14. American Physical Society, 2014.","mla":"Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>, vol. 113, no. 14, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>.","short":"M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014).","apa":"Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>","ista":"Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14)."},"publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/1403.0693","open_access":"1"}],"acknowledgement":"We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.\n\nM. S., M. K., and S. G. contributed equally to this work.","publication_status":"published","_id":"977","status":"public","date_created":"2018-12-11T11:49:30Z","doi":"10.1103/PhysRevLett.113.147204","oa":1,"year":"2014","quality_controlled":0,"day":"03","issue":"14","title":"Interferometric probes of many-body localization","publist_id":"6421","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"},{"first_name":"Michael","last_name":"Knap","full_name":"Knap, Michael J"},{"full_name":"Gopalakrishnan, Sarang","first_name":"Sarang","last_name":"Gopalakrishnan"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"},{"full_name":"Yao, Norman Y","last_name":"Yao","first_name":"Norman"},{"first_name":"Chris","last_name":"Laumann","full_name":"Laumann, Chris R"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"},{"full_name":"Lukin, Mikhail D","first_name":"Mikhail","last_name":"Lukin"},{"full_name":"Demler, Eugene A","last_name":"Demler","first_name":"Eugene"}],"volume":113,"publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems."}],"date_published":"2014-10-03T00:00:00Z","intvolume":"       113","extern":1},{"date_published":"2014-08-01T00:00:00Z","abstract":[{"text":"The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.","lang":"eng"}],"publication":"Nature Physics","volume":10,"author":[{"last_name":"Zeljkovic","first_name":"Ilija","full_name":"Zeljkovic, Ilija"},{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"first_name":"Chengyi","last_name":"Huang","full_name":"Huang, Chengyi"},{"full_name":"Sankar, Raman","first_name":"Raman","last_name":"Sankar"},{"first_name":"Daniel","last_name":"Walkup","full_name":"Walkup, Daniel"},{"full_name":"Zhou, Wenwen","last_name":"Zhou","first_name":"Wenwen"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"},{"full_name":"Chou, Fangcheng","first_name":"Fangcheng","last_name":"Chou"},{"first_name":"Wei","last_name":"Tsai","full_name":"Tsai, Wei-Feng"},{"last_name":"Lin","first_name":"Hsin","full_name":"Lin, Hsin"},{"full_name":"Bansil, Arun","last_name":"Bansil","first_name":"Arun"},{"last_name":"Fu","first_name":"Liang","full_name":"Fu, Liang"},{"full_name":"Hasan, Md Z","first_name":"Md","last_name":"Hasan"},{"full_name":"Madhavan, Vidya","first_name":"Vidya","last_name":"Madhavan"}],"publist_id":"6423","title":"Mapping the unconventional orbital texture in topological crystalline insulators","extern":1,"intvolume":"        10","page":"572 - 577","status":"public","doi":"10.1038/nphys3012","date_created":"2018-12-11T11:49:30Z","_id":"978","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1312.0164","open_access":"1"}],"acknowledgement":"V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105 for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231. W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009. W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","publisher":"Nature Publishing Group","citation":{"ama":"Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. 2014;10(8):572-577. doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>.","short":"I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn, F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics 10 (2014) 572–577.","mla":"Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>, vol. 10, no. 8, Nature Publishing Group, 2014, pp. 572–77, doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>.","ieee":"I. Zeljkovic <i>et al.</i>, “Mapping the unconventional orbital texture in topological crystalline insulators,” <i>Nature Physics</i>, vol. 10, no. 8. Nature Publishing Group, pp. 572–577, 2014.","apa":"Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2014). Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>","ista":"Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 10(8), 572–577."},"date_updated":"2021-01-12T08:22:23Z","month":"08","type":"journal_article","issue":"8","day":"01","quality_controlled":0,"year":"2014","oa":1},{"title":"Symmetry breaking and Landau quantization in topological crystalline insulators","publist_id":"6422","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym"},{"last_name":"Fu","first_name":"Liang","full_name":"Fu, Liang"}],"abstract":[{"lang":"eng","text":"In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators."}],"publication":"Physical Review B - Condensed Matter and Materials Physics","volume":90,"date_published":"2014-07-03T00:00:00Z","intvolume":"        90","extern":1,"date_updated":"2021-01-12T08:22:23Z","month":"07","type":"journal_article","publisher":"American Physical Society","citation":{"mla":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>.","ieee":"M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological crystalline insulators,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3. American Physical Society, 2014.","short":"M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","chicago":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>.","ama":"Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>","ista":"Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 90(3).","apa":"Serbyn, M., &#38; Fu, L. (2014). Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>"},"acknowledgement":"We thank V. Madhavan and Y. Okada for related collaborations, and P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR 1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0010526.","main_file_link":[{"url":"https://arxiv.org/abs/1403.8153","open_access":"1"}],"doi":"10.1103/PhysRevB.90.035402","status":"public","date_created":"2018-12-11T11:49:31Z","_id":"979","publication_status":"published","oa":1,"year":"2014","day":"03","issue":"3","quality_controlled":0},{"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","citation":{"ista":"Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586.","apa":"Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., &#38; Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>","short":"A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586.","ieee":"A. P. Higginbotham <i>et al.</i>, “Hole spin coherence in a Ge/Si heterostructure nanowire,” <i>Nano Letters</i>, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014.","mla":"Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>.","ama":"Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. 2014;14(6):3582-3586. doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>","chicago":"Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>."},"acknowledgement":"Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.2093"}],"_id":"98","date_created":"2018-12-11T11:44:37Z","doi":"10.1021/nl501242b","oa":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","issue":"6","title":"Hole spin coherence in a Ge/Si heterostructure nanowire","volume":14,"abstract":[{"lang":"eng","text":"Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing."}],"publication":"Nano Letters","page":"3582 - 3586","external_id":{"arxiv":["1403.2093"]},"arxiv":1,"date_updated":"2021-01-12T08:22:24Z","publisher":"American Chemical Society","publication_status":"published","status":"public","year":"2014","day":"05","publist_id":"7956","author":[{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"full_name":"Larsen, Thorvald","last_name":"Larsen","first_name":"Thorvald"},{"full_name":"Yao, Jun","first_name":"Jun","last_name":"Yao"},{"last_name":"Yan","first_name":"Hao","full_name":"Yan, Hao"},{"first_name":"Charles","last_name":"Lieber","full_name":"Lieber, Charles"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"},{"first_name":"Ferdinand","last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand"}],"date_published":"2014-05-05T00:00:00Z","intvolume":"        14","extern":"1"},{"date_updated":"2021-01-12T08:22:24Z","month":"11","type":"journal_article","publisher":"American Physical Society","citation":{"ista":"Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2014). Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>","mla":"Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>.","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17. American Physical Society, 2014.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>.","ama":"Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1408.4105","open_access":"1"}],"acknowledgement":"Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.).","date_created":"2018-12-11T11:49:31Z","status":"public","doi":"10.1103/PhysRevB.90.174302","publication_status":"published","_id":"980","oa":1,"year":"2014","issue":"17","day":"06","quality_controlled":0,"title":"Quantum quenches in the many-body localized phase","publist_id":"6420","author":[{"orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"abstract":[{"text":"Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.","lang":"eng"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","volume":90,"date_published":"2014-11-06T00:00:00Z","intvolume":"        90","extern":1},{"date_published":"2014-09-01T00:00:00Z","author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"first_name":"Rudiger","last_name":"Urbanke","full_name":"Urbanke, Rudiger"}],"intvolume":"        62","extern":"1","publication_status":"published","status":"public","date_updated":"2021-01-12T08:08:46Z","publisher":"IEEE","year":"2014","day":"01","volume":62,"abstract":[{"lang":"eng","text":"We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel."}],"publication":"IEEE Transactions on Communications","title":"From polar to Reed-Muller codes: A technique to improve the finite-length performance","arxiv":1,"external_id":{"arxiv":["1401.3127"]},"page":"3084-3091","main_file_link":[{"url":"https://arxiv.org/abs/1401.3127","open_access":"1"}],"_id":"6739","publication_identifier":{"issn":["0090-6778"]},"doi":"10.1109/tcomm.2014.2345069","date_created":"2019-07-31T07:20:21Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","citation":{"apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2014). From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>","ista":"Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. 62(9), 3084–3091.","ama":"Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. 2014;62(9):3084-3091. doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications 62 (2014) 3084–3091.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes: A technique to improve the finite-length performance,” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014.","mla":"Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9, IEEE, 2014, pp. 3084–91, doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>."},"language":[{"iso":"eng"}],"quality_controlled":"1","issue":"9","oa_version":"Preprint","oa":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","day":"01","year":"2014","oa_version":"Preprint","oa":1,"publication_status":"published","_id":"6740","publication_identifier":{"eisbn":["978-1-4799-8009-3"]},"related_material":{"record":[{"status":"public","relation":"later_version","id":"6678"}]},"status":"public","doi":"10.1109/allerton.2014.7028535","date_created":"2019-07-31T07:24:23Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.7373"}],"citation":{"apa":"Mondelli, M., Urbanke, R., &#38; Hassani, H. (2014). How to achieve the capacity of asymmetric channels. In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i> (pp. 789–796). Monticello, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>","ista":"Mondelli M, Urbanke R, Hassani H. 2014. How to achieve the capacity of asymmetric channels. 52nd Annual Allerton Conference on Communication, Control, and Computing. Allerton Conference on Communication, Control, and Computing, 789–796.","ama":"Mondelli M, Urbanke R, Hassani H. How to achieve the capacity of asymmetric channels. In: <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>. IEEE; 2014:789-796. doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>","chicago":"Mondelli, Marco, Rudiger Urbanke, and Hamed Hassani. “How to Achieve the Capacity of Asymmetric Channels.” In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, 789–96. IEEE, 2014. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>.","short":"M. Mondelli, R. Urbanke, H. Hassani, in:, 52nd Annual Allerton Conference on Communication, Control, and Computing, IEEE, 2014, pp. 789–796.","mla":"Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, IEEE, 2014, pp. 789–96, doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>.","ieee":"M. Mondelli, R. Urbanke, and H. Hassani, “How to achieve the capacity of asymmetric channels,” in <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, Monticello, IL, United States, 2014, pp. 789–796."},"publisher":"IEEE","type":"conference","date_updated":"2023-02-23T12:49:36Z","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","arxiv":1,"external_id":{"arxiv":["1406.7373"]},"page":"789-796","conference":{"end_date":"2014-10-03","start_date":"2014-09-30","name":"Allerton Conference on Communication, Control, and Computing","location":"Monticello, IL, United States"},"date_published":"2014-10-01T00:00:00Z","abstract":[{"text":"We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions.","lang":"eng"}],"publication":"52nd Annual Allerton Conference on Communication, Control, and Computing","author":[{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"full_name":"Urbanke, Rudiger","first_name":"Rudiger","last_name":"Urbanke"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"}],"title":"How to achieve the capacity of asymmetric channels"},{"language":[{"iso":"eng"}],"quality_controlled":"1","day":"20","issue":"3","year":"2014","oa_version":"None","publication_status":"published","_id":"6744","status":"public","date_created":"2019-07-31T09:05:07Z","doi":"10.1109/twc.2014.020914.130669","publisher":"IEEE","citation":{"ieee":"M. Mondelli, Q. Zhou, V. Lottici, and X. Ma, “Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications,” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3. IEEE, pp. 1397–1409, 2014.","mla":"Mondelli, Marco, et al. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3, IEEE, 2014, pp. 1397–409, doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>.","short":"M. Mondelli, Q. Zhou, V. Lottici, X. Ma, IEEE Transactions on Wireless Communications 13 (2014) 1397–1409.","chicago":"Mondelli, Marco, Qi Zhou, Vincenzo Lottici, and Xiaoli Ma. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>.","ama":"Mondelli M, Zhou Q, Lottici V, Ma X. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. 2014;13(3):1397-1409. doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>","ista":"Mondelli M, Zhou Q, Lottici V, Ma X. 2014. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. 13(3), 1397–1409.","apa":"Mondelli, M., Zhou, Q., Lottici, V., &#38; Ma, X. (2014). Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:08:48Z","month":"03","extern":"1","intvolume":"        13","page":"1397-1409","date_published":"2014-03-20T00:00:00Z","volume":13,"publication":"IEEE Transactions on Wireless Communications","abstract":[{"text":"With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods.","lang":"eng"}],"author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"full_name":"Zhou, Qi","first_name":"Qi","last_name":"Zhou"},{"full_name":"Lottici, Vincenzo","last_name":"Lottici","first_name":"Vincenzo"},{"first_name":"Xiaoli","last_name":"Ma","full_name":"Ma, Xiaoli"}],"title":"Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications"},{"department":[{"_id":"HeEd"}],"oa_version":"None","quality_controlled":"1","language":[{"iso":"eng"}],"day":"01","year":"2014","citation":{"ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>.","ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014.","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p."},"publisher":"Springer Nature","series_title":"SpringerBriefs in Applied Sciences and Technology","scopus_import":"1","type":"book","date_updated":"2022-03-04T07:47:54Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106","relation":"other","description":"available as eBook via catalog IST BookList"},{"description":"available via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842","relation":"other"}]},"_id":"6853","publication_identifier":{"issn":["2191-530X"],"isbn":["9-783-3190-5956-3"],"eissn":["2191-5318"],"eisbn":["9-783-3190-5957-0"]},"publication_status":"published","doi":"10.1007/978-3-319-05957-0","status":"public","date_created":"2019-09-06T09:22:33Z","place":"Cham","article_processing_charge":"No","page":"IX, 110","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"}],"title":"A Short Course in Computational Geometry and Topology","date_published":"2014-01-01T00:00:00Z","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"edition":"1","abstract":[{"text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.","lang":"eng"}]}]