[{"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       113","publisher":"Proceedings of the National Academy of Sciences","date_published":"2016-10-13T00:00:00Z","extern":"1","external_id":{"pmid":["27821763"]},"scopus_import":"1","date_created":"2023-09-06T12:53:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","page":"E7456-E7463","publication":"PNAS","date_updated":"2023-11-07T11:53:06Z","year":"2016","volume":113,"article_processing_charge":"No","oa_version":"Published Version","day":"13","citation":{"chicago":"Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai, Florian M Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>.","mla":"Martin, Thomas G., et al. “Design of a Molecular Support for Cryo-EM Structure Determination.” <i>PNAS</i>, vol. 113, no. 47, Proceedings of the National Academy of Sciences, 2016, pp. E7456–63, doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>.","apa":"Martin, T. G., Bharat, T. A. M., Joerger, A. C., Bai, X., Praetorius, F. M., Fersht, A. R., … Scheres, S. H. W. (2016). Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612720113\">https://doi.org/10.1073/pnas.1612720113</a>","ieee":"T. G. Martin <i>et al.</i>, “Design of a molecular support for cryo-EM structure determination,” <i>PNAS</i>, vol. 113, no. 47. Proceedings of the National Academy of Sciences, pp. E7456–E7463, 2016.","ama":"Martin TG, Bharat TAM, Joerger AC, et al. Design of a molecular support for cryo-EM structure determination. <i>PNAS</i>. 2016;113(47):E7456-E7463. doi:<a href=\"https://doi.org/10.1073/pnas.1612720113\">10.1073/pnas.1612720113</a>","ista":"Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius FM, Fersht AR, Dietz H, Scheres SHW. 2016. Design of a molecular support for cryo-EM structure determination. PNAS. 113(47), E7456–E7463.","short":"T.G. Martin, T.A.M. Bharat, A.C. Joerger, X. Bai, F.M. Praetorius, A.R. Fersht, H. Dietz, S.H.W. Scheres, PNAS 113 (2016) E7456–E7463."},"pmid":1,"month":"10","publication_status":"published","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"47","abstract":[{"text":"Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.","lang":"eng"}],"doi":"10.1073/pnas.1612720113","author":[{"last_name":"Martin","full_name":"Martin, Thomas G.","first_name":"Thomas G."},{"full_name":"Bharat, Tanmay A. M.","last_name":"Bharat","first_name":"Tanmay A. M."},{"first_name":"Andreas C.","full_name":"Joerger, Andreas C.","last_name":"Joerger"},{"last_name":"Bai","full_name":"Bai, Xiao-chen","first_name":"Xiao-chen"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Alan R.","last_name":"Fersht","full_name":"Fersht, Alan R."},{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"},{"full_name":"Scheres, Sjors H. W.","last_name":"Scheres","first_name":"Sjors H. W."}],"title":"Design of a molecular support for cryo-EM structure determination","_id":"14304"},{"extern":"1","date_published":"2016-02-06T00:00:00Z","date_created":"2021-01-19T11:11:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"        19","publisher":"Elsevier","year":"2016","keyword":["General Chemistry","General Chemical Engineering"],"oa":1,"article_type":"original","page":"19-27","publication":"Comptes Rendus Chimie","date_updated":"2023-02-23T13:46:55Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","day":"06","citation":{"mla":"Bakail, May M., and Francoise Ochsenbein. “Targeting Protein–Protein Interactions, a Wide Open Field for Drug Design.” <i>Comptes Rendus Chimie</i>, vol. 19, no. 1–2, Elsevier, 2016, pp. 19–27, doi:<a href=\"https://doi.org/10.1016/j.crci.2015.12.004\">10.1016/j.crci.2015.12.004</a>.","chicago":"Bakail, May M, and Francoise Ochsenbein. “Targeting Protein–Protein Interactions, a Wide Open Field for Drug Design.” <i>Comptes Rendus Chimie</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.crci.2015.12.004\">https://doi.org/10.1016/j.crci.2015.12.004</a>.","apa":"Bakail, M. M., &#38; Ochsenbein, F. (2016). Targeting protein–protein interactions, a wide open field for drug design. <i>Comptes Rendus Chimie</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.crci.2015.12.004\">https://doi.org/10.1016/j.crci.2015.12.004</a>","ieee":"M. M. Bakail and F. Ochsenbein, “Targeting protein–protein interactions, a wide open field for drug design,” <i>Comptes Rendus Chimie</i>, vol. 19, no. 1–2. Elsevier, pp. 19–27, 2016.","short":"M.M. Bakail, F. Ochsenbein, Comptes Rendus Chimie 19 (2016) 19–27.","ama":"Bakail MM, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. <i>Comptes Rendus Chimie</i>. 2016;19(1-2):19-27. doi:<a href=\"https://doi.org/10.1016/j.crci.2015.12.004\">10.1016/j.crci.2015.12.004</a>","ista":"Bakail MM, Ochsenbein F. 2016. Targeting protein–protein interactions, a wide open field for drug design. Comptes Rendus Chimie. 19(1–2), 19–27."},"file_date_updated":"2021-01-22T12:36:52Z","month":"02","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","volume":19,"file":[{"relation":"main_file","creator":"dernst","file_size":2045260,"file_name":"2016_ComptesRendueChimie_Bakail.pdf","content_type":"application/pdf","checksum":"c262814ffdbfe95900256ab9ff42cdf5","access_level":"open_access","date_updated":"2021-01-22T12:36:52Z","success":1,"date_created":"2021-01-22T12:36:52Z","file_id":"9035"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"issue":"1-2","abstract":[{"lang":"eng","text":"Targeting protein–protein interactions has long been considered as a very difficult if impossible task, but over the past decade, front lines have moved. The number of successful examples is exponentially growing. This review presents a rapid overview of recent advances in this field considering the strengths and weaknesses of the small molecule approaches and alternative strategies such as the selection or design of artificial antibodies, peptides or peptidomimetics."},{"text":"Cibler les interactions protéine–protéine a longtemps été considéré comme une tâche très difficile, voire impossible, mais, depuis les dix dernières années, les lignes ont bougé. Le nombre d’exemples de réussites s’accroît exponentiellement. Cette revue présente un rapide panorama des avancées récentes dans ce domaine, considérant les forces et les faiblesses de l’approche « petite molécule » ainsi que des stratégies alternatives comme la sélection ou le design d’anticorps artificiels, de peptides ou de peptidomimétiques.","lang":"fre"}],"doi":"10.1016/j.crci.2015.12.004","author":[{"orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail","full_name":"Bakail, May M"},{"first_name":"Francoise","full_name":"Ochsenbein, Francoise","last_name":"Ochsenbein"}],"title":"Targeting protein–protein interactions, a wide open field for drug design","_id":"9019","publication_status":"published","status":"public","publication_identifier":{"issn":["1631-0748"]}},{"article_processing_charge":"No","volume":12,"arxiv":1,"oa_version":"Preprint","day":"28","citation":{"mla":"Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” <i>Soft Matter</i>, vol. 12, no. 20, Royal Society of Chemistry, 2016, pp. 4584–89, doi:<a href=\"https://doi.org/10.1039/c5sm03127c\">10.1039/c5sm03127c</a>.","chicago":"Davies Wykes, Megan S., Jérémie A Palacci, Takuji Adachi, Leif Ristroph, Xiao Zhong, Michael D. Ward, Jun Zhang, and Michael J. Shelley. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c5sm03127c\">https://doi.org/10.1039/c5sm03127c</a>.","ama":"Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale rotors and swimmers. <i>Soft Matter</i>. 2016;12(20):4584-4589. doi:<a href=\"https://doi.org/10.1039/c5sm03127c\">10.1039/c5sm03127c</a>","ista":"Davies Wykes MS, Palacci JA, Adachi T, Ristroph L, Zhong X, Ward MD, Zhang J, Shelley MJ. 2016. Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. 12(20), 4584–4589.","short":"M.S. Davies Wykes, J.A. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward, J. Zhang, M.J. Shelley, Soft Matter 12 (2016) 4584–4589.","apa":"Davies Wykes, M. S., Palacci, J. A., Adachi, T., Ristroph, L., Zhong, X., Ward, M. D., … Shelley, M. J. (2016). Dynamic self-assembly of microscale rotors and swimmers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5sm03127c\">https://doi.org/10.1039/c5sm03127c</a>","ieee":"M. S. Davies Wykes <i>et al.</i>, “Dynamic self-assembly of microscale rotors and swimmers,” <i>Soft Matter</i>, vol. 12, no. 20. Royal Society of Chemistry, pp. 4584–4589, 2016."},"pmid":1,"month":"05","status":"public","publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"issue":"20","abstract":[{"text":"Biological systems often involve the self-assembly of basic components into complex and functioning structures. Artificial systems that mimic such processes can provide a well-controlled setting to explore the principles involved and also synthesize useful micromachines. Our experiments show that immotile, but active, components self-assemble into two types of structure that exhibit the fundamental forms of motility: translation and rotation. Specifically, micron-scale metallic rods are designed to induce extensile surface flows in the presence of a chemical fuel; these rods interact with each other and pair up to form either a swimmer or a rotor. Such pairs can transition reversibly between these two configurations, leading to kinetics reminiscent of bacterial run-and-tumble motion.","lang":"eng"}],"doi":"10.1039/c5sm03127c","author":[{"last_name":"Davies Wykes","full_name":"Davies Wykes, Megan S.","first_name":"Megan S."},{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"last_name":"Adachi","full_name":"Adachi, Takuji","first_name":"Takuji"},{"first_name":"Leif","full_name":"Ristroph, Leif","last_name":"Ristroph"},{"first_name":"Xiao","last_name":"Zhong","full_name":"Zhong, Xiao"},{"first_name":"Michael D.","full_name":"Ward, Michael D.","last_name":"Ward"},{"first_name":"Jun","last_name":"Zhang","full_name":"Zhang, Jun"},{"first_name":"Michael J.","last_name":"Shelley","full_name":"Shelley, Michael J."}],"title":"Dynamic self-assembly of microscale rotors and swimmers","_id":"9051","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06330"}],"publisher":"Royal Society of Chemistry","extern":"1","external_id":{"pmid":["27121100"],"arxiv":["1509.06330"]},"date_published":"2016-05-28T00:00:00Z","scopus_import":"1","date_created":"2021-02-01T13:44:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","page":"4584-4589","publication":"Soft Matter","date_updated":"2023-02-23T13:47:38Z","year":"2016","oa":1},{"article_type":"original","page":"6357-6364","publication":"Soft Matter","date_updated":"2023-02-23T13:47:40Z","year":"2016","keyword":["General Chemistry","Condensed Matter Physics"],"oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        12","main_file_link":[{"url":"https://arxiv.org/abs/1609.01497","open_access":"1"}],"publisher":"Royal Society of Chemistry ","date_published":"2016-08-14T00:00:00Z","external_id":{"pmid":["27338294"],"arxiv":["1609.01497"]},"extern":"1","scopus_import":"1","date_created":"2021-02-01T13:44:15Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"issue":"30","abstract":[{"lang":"eng","text":"We describe colloidal Janus particles with metallic and dielectric faces that swim vigorously when illuminated by defocused optical tweezers without consuming any chemical fuel. Rather than wandering randomly, these optically-activated colloidal swimmers circulate back and forth through the beam of light, tracing out sinuous rosette patterns. We propose a model for this mode of light-activated transport that accounts for the observed behavior through a combination of self-thermophoresis and optically-induced torque. In the deterministic limit, this model yields trajectories that resemble rosette curves known as hypotrochoids."}],"doi":"10.1039/c6sm01163b","author":[{"first_name":"Henrique","last_name":"Moyses","full_name":"Moyses, Henrique"},{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"},{"first_name":"Stefano","full_name":"Sacanna, Stefano","last_name":"Sacanna"},{"first_name":"David G.","last_name":"Grier","full_name":"Grier, David G."}],"title":"Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam","_id":"9052","article_processing_charge":"No","volume":12,"arxiv":1,"oa_version":"Preprint","day":"14","citation":{"ista":"Moyses H, Palacci JA, Sacanna S, Grier DG. 2016. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. 12(30), 6357–6364.","short":"H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364.","ama":"Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. <i>Soft Matter</i>. 2016;12(30):6357-6364. doi:<a href=\"https://doi.org/10.1039/c6sm01163b\">10.1039/c6sm01163b</a>","apa":"Moyses, H., Palacci, J. A., Sacanna, S., &#38; Grier, D. G. (2016). Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c6sm01163b\">https://doi.org/10.1039/c6sm01163b</a>","ieee":"H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam,” <i>Soft Matter</i>, vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016.","mla":"Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” <i>Soft Matter</i>, vol. 12, no. 30, Royal Society of Chemistry , 2016, pp. 6357–64, doi:<a href=\"https://doi.org/10.1039/c6sm01163b\">10.1039/c6sm01163b</a>.","chicago":"Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” <i>Soft Matter</i>. Royal Society of Chemistry , 2016. <a href=\"https://doi.org/10.1039/c6sm01163b\">https://doi.org/10.1039/c6sm01163b</a>."},"month":"08","pmid":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"American Geophysical Union","intvolume":"       121","main_file_link":[{"url":"https://doi.org/10.1002/2015JD023497","open_access":"1"}],"date_published":"2016-03-16T00:00:00Z","extern":"1","date_created":"2021-02-15T14:21:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"3100-3119","article_type":"original","publication":"Journal of Geophysical Research: Atmospheres","date_updated":"2022-01-24T13:41:02Z","year":"2016","oa":1,"volume":121,"article_processing_charge":"No","oa_version":"Published Version","citation":{"chicago":"Drobinski, P., B. Alonzo, S. Bastin, N. Da Silva, and Caroline J Muller. “Scaling of Precipitation Extremes with Temperature in the French Mediterranean Region: What Explains the Hook Shape?” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2016. <a href=\"https://doi.org/10.1002/2015jd023497\">https://doi.org/10.1002/2015jd023497</a>.","mla":"Drobinski, P., et al. “Scaling of Precipitation Extremes with Temperature in the French Mediterranean Region: What Explains the Hook Shape?” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 121, no. 7, American Geophysical Union, 2016, pp. 3100–19, doi:<a href=\"https://doi.org/10.1002/2015jd023497\">10.1002/2015jd023497</a>.","ieee":"P. Drobinski, B. Alonzo, S. Bastin, N. D. Silva, and C. J. Muller, “Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape?,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 121, no. 7. American Geophysical Union, pp. 3100–3119, 2016.","apa":"Drobinski, P., Alonzo, B., Bastin, S., Silva, N. D., &#38; Muller, C. J. (2016). Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2015jd023497\">https://doi.org/10.1002/2015jd023497</a>","ama":"Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? <i>Journal of Geophysical Research: Atmospheres</i>. 2016;121(7):3100-3119. doi:<a href=\"https://doi.org/10.1002/2015jd023497\">10.1002/2015jd023497</a>","short":"P. Drobinski, B. Alonzo, S. Bastin, N.D. Silva, C.J. Muller, Journal of Geophysical Research: Atmospheres 121 (2016) 3100–3119.","ista":"Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. 2016. Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? Journal of Geophysical Research: Atmospheres. 121(7), 3100–3119."},"day":"16","month":"03","publication_status":"published","status":"public","publication_identifier":{"issn":["2169-897X","2169-8996"]},"abstract":[{"lang":"eng","text":"Expected changes to future extreme precipitation remain a key uncertainty associated with anthropogenic climate change. Extreme precipitation has been proposed to scale with the precipitable water content in the atmosphere. Assuming constant relative humidity, this implies an increase of precipitation extremes at a rate of about 7% °C−1 globally as indicated by the Clausius‐Clapeyron relationship. Increases faster and slower than Clausius‐Clapeyron have also been reported. In this work, we examine the scaling between precipitation extremes and temperature in the present climate using simulations and measurements from surface weather stations collected in the frame of the HyMeX and MED‐CORDEX programs in Southern France. Of particular interest are departures from the Clausius‐Clapeyron thermodynamic expectation, their spatial and temporal distribution, and their origin. Looking at the scaling of precipitation extreme with temperature, two regimes emerge which form a hook shape: one at low temperatures (cooler than around 15°C) with rates of increase close to the Clausius‐Clapeyron rate and one at high temperatures (warmer than about 15°C) with sub‐Clausius‐Clapeyron rates and most often negative rates. On average, the region of focus does not seem to exhibit super Clausius‐Clapeyron behavior except at some stations, in contrast to earlier studies. Many factors can contribute to departure from Clausius‐Clapeyron scaling: time and spatial averaging, choice of scaling temperature (surface versus condensation level), and precipitation efficiency and vertical velocity in updrafts that are not necessarily constant with temperature. But most importantly, the dynamical contribution of orography to precipitation in the fall over this area during the so‐called “Cevenoles” events, explains the hook shape of the scaling of precipitation extremes."}],"issue":"7","doi":"10.1002/2015jd023497","title":"Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape?","author":[{"full_name":"Drobinski, P.","last_name":"Drobinski","first_name":"P."},{"last_name":"Alonzo","full_name":"Alonzo, B.","first_name":"B."},{"first_name":"S.","last_name":"Bastin","full_name":"Bastin, S."},{"first_name":"N. Da","full_name":"Silva, N. Da","last_name":"Silva"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350"}],"_id":"9140"},{"intvolume":"       120","publisher":"American Chemical Society","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","volume":120,"month":"12","publist_id":"7962","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"05","citation":{"chicago":"Cole, Jaqueline, Tzechia Lin, Christopher Ashcroft, Javier Pérez Moreno, Yizhou Tan, Perumal Venkatesan, Andrew P Higginbotham, et al. “Relating the Structure of Geminal Amido Esters to Their Molecular Hyperpolarizability.” <i>Journal of Physical Chemistry C</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.jpcc.6b10724\">https://doi.org/10.1021/acs.jpcc.6b10724</a>.","mla":"Cole, Jaqueline, et al. “Relating the Structure of Geminal Amido Esters to Their Molecular Hyperpolarizability.” <i>Journal of Physical Chemistry C</i>, vol. 120, no. 51, American Chemical Society, 2016, pp. 29439–48, doi:<a href=\"https://doi.org/10.1021/acs.jpcc.6b10724\">10.1021/acs.jpcc.6b10724</a>.","ama":"Cole J, Lin T, Ashcroft C, et al. Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. <i>Journal of Physical Chemistry C</i>. 2016;120(51):29439-29448. doi:<a href=\"https://doi.org/10.1021/acs.jpcc.6b10724\">10.1021/acs.jpcc.6b10724</a>","ista":"Cole J, Lin T, Ashcroft C, Pérez Moreno J, Tan Y, Venkatesan P, Higginbotham AP, Pattison P, Edwards A, Piltz R, Clays K, Ilangovan A. 2016. Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. Journal of Physical Chemistry C. 120(51), 29439–29448.","short":"J. Cole, T. Lin, C. Ashcroft, J. Pérez Moreno, Y. Tan, P. Venkatesan, A.P. Higginbotham, P. Pattison, A. Edwards, R. Piltz, K. Clays, A. Ilangovan, Journal of Physical Chemistry C 120 (2016) 29439–29448.","apa":"Cole, J., Lin, T., Ashcroft, C., Pérez Moreno, J., Tan, Y., Venkatesan, P., … Ilangovan, A. (2016). Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. <i>Journal of Physical Chemistry C</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcc.6b10724\">https://doi.org/10.1021/acs.jpcc.6b10724</a>","ieee":"J. Cole <i>et al.</i>, “Relating the structure of geminal Amido Esters to their molecular hyperpolarizability,” <i>Journal of Physical Chemistry C</i>, vol. 120, no. 51. American Chemical Society, pp. 29439–29448, 2016."},"date_created":"2018-12-11T11:44:35Z","oa_version":"None","extern":"1","date_published":"2016-12-05T00:00:00Z","date_updated":"2021-01-12T08:21:55Z","publication":"Journal of Physical Chemistry C","page":"29439 - 29448","status":"public","publication_status":"published","acknowledgement":"J.M.C. thanks the 1851 Royal Commission of the Great Exhibition for a Design Fellowship, hosted by Argonne National Laboratory where work done was supported by the DOE Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. T.-C.L acknowledges the Taiwanese Government for a Studying Abroad Scholarship. C.M.A is indebted to the EPSRC UK for a DTA Ph.D. studentship (Grants EP/J500380/1 and EP/L504920/1). Y.T. is grateful for a Cavendish-NUDT Scholarship. The Swiss-Norwegian Collaborative Research Group at the ESRF, Grenoble, France, is thanked for access to synchrotron facilities. The OPAL reactor, ANSTO, Australia, is acknowledged for access to neutron scattering facilities via a program proposal, ID 1236. J.P-M. is grateful to Skidmore College for supporting this work via a full-year sabbatical with enhancement. All authors thank the EPSRC UK National Service for Computational Chemistry Software (NSCCS) and acknowledge contributions from its staff in supporting this work.","_id":"92","author":[{"full_name":"Cole, Jaqueline","last_name":"Cole","first_name":"Jaqueline"},{"full_name":"Lin, Tzechia","last_name":"Lin","first_name":"Tzechia"},{"last_name":"Ashcroft","full_name":"Ashcroft, Christopher","first_name":"Christopher"},{"last_name":"Pérez Moreno","full_name":"Pérez Moreno, Javier","first_name":"Javier"},{"full_name":"Tan, Yizhou","last_name":"Tan","first_name":"Yizhou"},{"last_name":"Venkatesan","full_name":"Venkatesan, Perumal","first_name":"Perumal"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"first_name":"Philip","full_name":"Pattison, Philip","last_name":"Pattison"},{"first_name":"Alison","full_name":"Edwards, Alison","last_name":"Edwards"},{"first_name":"Ross","full_name":"Piltz, Ross","last_name":"Piltz"},{"first_name":"Koen","full_name":"Clays, Koen","last_name":"Clays"},{"full_name":"Ilangovan, Andivelu","last_name":"Ilangovan","first_name":"Andivelu"}],"title":"Relating the structure of geminal Amido Esters to their molecular hyperpolarizability","doi":"10.1021/acs.jpcc.6b10724","issue":"51","year":"2016","abstract":[{"text":"Advanced organic nonlinear optical (NLO) materials have attracted increasing attention due to their multitude of applications in modern telecommunication devices. Arguably the most important advantage of organic NLO materials, relative to traditionally used inorganic NLO materials, is their short optical response time. Geminal amido esters with their donor-π-acceptor (D-π-A) architecture exhibit high levels of electron delocalization and substantial intramolecular charge transfer, which should endow these materials with short optical response times and large molecular (hyper)polarizabilities. In order to test this hypothesis, the linear and second-order nonlinear optical properties of five geminal amido esters, (E)-ethyl 3-(X-phenylamino)-2-(Y-phenylcarbamoyl)acrylate (1, X = 4-H, Y = 4-H; 2, X = 4-CH3, Y = 4-CH3; 3, X = 4-NO2, Y = 2,5-OCH3; 4, X = 2-Cl, Y = 2-Cl; 5, X = 4-Cl, Y = 4-Cl) were synthesized and characterized, whereby NLO structure-function relationships were established including intramolecular charge transfer characteristics, crystal field effects, and molecular first hyperpolarizabilities (β). Given the typically large errors (10-30%) associated with the determination of β coefficients, three independent methods were used: (i) density functional theory, (ii) hyper-Rayleigh scattering, and (iii) high-resolution X-ray diffraction data analysis based on multipolar modeling of electron densities at each atom. These three methods delivered consistent values of β, and based on these results, 3 should hold the most promise for NLO applications. The correlation between the molecular structure of these geminal amido esters and their linear and nonlinear optical properties thus provide molecular design guidelines for organic NLO materials; this leads to the ultimate goal of generating bespoke organic molecules to suit a given NLO device application.","lang":"eng"}]},{"author":[{"last_name":"Sánchez Danés","full_name":"Sánchez Danés, Adriana","first_name":"Adriana"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"last_name":"Larsimont","full_name":"Larsimont, Jean","first_name":"Jean"},{"last_name":"Liagre","full_name":"Liagre, Mélanie","first_name":"Mélanie"},{"first_name":"Khalil","full_name":"Youssef, Khalil","last_name":"Youssef"},{"last_name":"Simons","full_name":"Simons, Benjamin","first_name":"Benjamin"},{"first_name":"Cédric","last_name":"Blanpain","full_name":"Blanpain, Cédric"}],"title":"Defining the clonal dynamics leading to mouse skin tumour initiation","_id":"930","year":"2016","issue":"7616","abstract":[{"text":"The changes in cell dynamics after oncogenic mutation that lead to the development of tumours are currently unknown. Here, using skin epidermis as a model, we assessed the effect of oncogenic hedgehog signalling in distinct cell populations and their capacity to induce basal cell carcinoma, the most frequent cancer in humans. We found that only stem cells, and not progenitors, initiated tumour formation upon oncogenic hedgehog signalling. This difference was due to the hierarchical organization of tumour growth in oncogene-targeted stem cells, characterized by an increase in symmetric self-renewing divisions and a higher p53-dependent resistance to apoptosis, leading to rapid clonal expansion and progression into invasive tumours. Our work reveals that the capacity of oncogene-targeted cells to induce tumour formation is dependent not only on their long-term survival and expansion, but also on the specific clonal dynamics of the cancer cell of origin.","lang":"eng"}],"doi":"10.1038/nature19069","publication":"Nature","date_updated":"2021-01-12T08:21:59Z","status":"public","publication_status":"published","acknowledgement":"We would like to thank J.-M. Vanderwinden and the LiMiF for the help with confocal microscopy. C.B. is an investigator of WELBIO. A.S.-D. and J.C.L. are supported by a fellowship of the FNRS and FRIA respectively. B.D.S. and E.H. are supported by the Wellcome Trust (grant numbers 098357/Z/12/Z and 110326/Z/15/Z). E.H. is supported by a fellowship from Trinity College, Cambridge. This work was supported by the FNRS, the IUAP program, the Fondation contre le Cancer, the ULB fondation, the foundation Bettencourt Schueller, the foundation Baillet Latour, a consolidator grant of the European Research Council.","page":"298 - 303","day":"08","citation":{"mla":"Sánchez Danés, Adriana, et al. “Defining the Clonal Dynamics Leading to Mouse Skin Tumour Initiation.” <i>Nature</i>, vol. 536, no. 7616, Nature Publishing Group, 2016, pp. 298–303, doi:<a href=\"https://doi.org/10.1038/nature19069\">10.1038/nature19069</a>.","chicago":"Sánchez Danés, Adriana, Edouard B Hannezo, Jean Larsimont, Mélanie Liagre, Khalil Youssef, Benjamin Simons, and Cédric Blanpain. “Defining the Clonal Dynamics Leading to Mouse Skin Tumour Initiation.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature19069\">https://doi.org/10.1038/nature19069</a>.","ama":"Sánchez Danés A, Hannezo EB, Larsimont J, et al. Defining the clonal dynamics leading to mouse skin tumour initiation. <i>Nature</i>. 2016;536(7616):298-303. doi:<a href=\"https://doi.org/10.1038/nature19069\">10.1038/nature19069</a>","short":"A. Sánchez Danés, E.B. Hannezo, J. Larsimont, M. Liagre, K. Youssef, B. Simons, C. Blanpain, Nature 536 (2016) 298–303.","ista":"Sánchez Danés A, Hannezo EB, Larsimont J, Liagre M, Youssef K, Simons B, Blanpain C. 2016. Defining the clonal dynamics leading to mouse skin tumour initiation. Nature. 536(7616), 298–303.","ieee":"A. Sánchez Danés <i>et al.</i>, “Defining the clonal dynamics leading to mouse skin tumour initiation,” <i>Nature</i>, vol. 536, no. 7616. Nature Publishing Group, pp. 298–303, 2016.","apa":"Sánchez Danés, A., Hannezo, E. B., Larsimont, J., Liagre, M., Youssef, K., Simons, B., &#38; Blanpain, C. (2016). Defining the clonal dynamics leading to mouse skin tumour initiation. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature19069\">https://doi.org/10.1038/nature19069</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6508","month":"07","date_published":"2016-07-08T00:00:00Z","extern":"1","date_created":"2018-12-11T11:49:15Z","oa_version":"None","intvolume":"       536","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","volume":536},{"doi":"10.1103/PhysRevE.93.022405","abstract":[{"lang":"eng","text":"In many adult tissues, stem cells and differentiated cells are not homogeneously distributed: stem cells are arranged in periodic &quot;niches,&quot; and differentiated cells are constantly produced and migrate out of these niches. In this article, we provide a general theoretical framework to study mixtures of dividing and actively migrating particles, which we apply to biological tissues. We show in particular that the interplay between the stresses arising from active cell migration and stem cell division give rise to robust stem cell patterns. The instability of the tissue leads to spatial patterns which are either steady or oscillating in time. The wavelength of the instability has an order of magnitude consistent with the biological observations. We also discuss the implications of these results for future in vitro and in vivo experiments."}],"issue":"2","year":"2016","_id":"931","title":"Interplay of migratory and division forces as a generic mechanism for stem cell patterns","author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Alice","last_name":"Coucke","full_name":"Coucke, Alice"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}],"publication_status":"published","status":"public","acknowledgement":"The authors thank Jacques Prost and Pierre Recho for helpful discussions, as well as the Labex CelTisPhyBio and all its members. E.H. acknowledges for funding a Young Researcher Prize from the Bettencourt-Schueller Fondation, and a Junior Research Fellowship from Trinity College, Cambridge.","date_updated":"2021-01-12T08:22:00Z","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","oa_version":"None","date_created":"2018-12-11T11:49:16Z","date_published":"2016-02-28T00:00:00Z","extern":"1","publist_id":"6509","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","citation":{"chicago":"Hannezo, Edouard B, Alice Coucke, and Jean Joanny. “Interplay of Migratory and Division Forces as a Generic Mechanism for Stem Cell Patterns.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022405\">https://doi.org/10.1103/PhysRevE.93.022405</a>.","mla":"Hannezo, Edouard B., et al. “Interplay of Migratory and Division Forces as a Generic Mechanism for Stem Cell Patterns.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022405\">10.1103/PhysRevE.93.022405</a>.","short":"E.B. Hannezo, A. Coucke, J. Joanny, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","ista":"Hannezo EB, Coucke A, Joanny J. 2016. Interplay of migratory and division forces as a generic mechanism for stem cell patterns. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2).","ama":"Hannezo EB, Coucke A, Joanny J. Interplay of migratory and division forces as a generic mechanism for stem cell patterns. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022405\">10.1103/PhysRevE.93.022405</a>","ieee":"E. B. Hannezo, A. Coucke, and J. Joanny, “Interplay of migratory and division forces as a generic mechanism for stem cell patterns,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","apa":"Hannezo, E. B., Coucke, A., &#38; Joanny, J. (2016). Interplay of migratory and division forces as a generic mechanism for stem cell patterns. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022405\">https://doi.org/10.1103/PhysRevE.93.022405</a>"},"day":"28","volume":93,"article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"publisher":"American Institute of Physics","intvolume":"        93"},{"page":"24 - 35","acknowledgement":"We thank J. Bear, B. Goldstein, A. Ewald, and D. Soroldoni for critical reading. This work was funded by an EMBO Long Term Fellowship to J.S., a Research Fellowship from Trinity College, Cambridge and a Bettencourt-Schueller Foundation Young Researcher Prize to E.H., a Cancer Institute NSW Early Career Researcher fellowship (13/ECF/1–25) and a Cancer Australia/Cure Cancer Australia Foundation project grant (1070498) to M.B., and grants from the NHLBI (HL117164) and NIGMS (GM074104) to J.B.W. J.B.W. was an early career scientist of the Howard Hughes Medical Institute. This work was initiated at the New Quantitative Approaches to Morphogenesis Workshop at UCSB, which is funded in part by the National Science Foundation (PHY11-25915) and the NIGMS (GM067110-05).","status":"public","publication_status":"published","date_updated":"2021-01-12T08:22:00Z","publication":"Developmental Cell","doi":"10.1016/j.devcel.2015.12.013","year":"2016","issue":"1","abstract":[{"text":"Epithelial sheets are crucial components of all metazoan animals, enclosing organs and protecting the animal from its environment. Epithelial homeostasis poses unique challenges, as addition of new cells and loss of old cells must be achieved without disrupting the fluid-tight barrier and apicobasal polarity of the epithelium. Several studies have identified cell biological mechanisms underlying extrusion of cells from epithelia, but far less is known of the converse mechanism by which new cells are added. Here, we combine molecular, pharmacological, and laser-dissection experiments with theoretical modeling to characterize forces driving emergence of an apical surface as single nascent cells are added to a vertebrate epithelium in vivo. We find that this process involves the interplay between cell-autonomous actin-generated pushing forces in the emerging cell and mechanical properties of neighboring cells. Our findings define the forces driving this cell behavior, contributing to a more comprehensive understanding of epithelial homeostasis.","lang":"eng"}],"_id":"932","author":[{"first_name":"Jakub","last_name":"Sedzinski","full_name":"Sedzinski, Jakub"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Tu","full_name":"Tu, Fan","first_name":"Fan"},{"first_name":"Maté","last_name":"Biro","full_name":"Biro, Maté"},{"first_name":"John","full_name":"Wallingford, John","last_name":"Wallingford"}],"title":"Emergence of an Apical Epithelial Cell Surface In Vivo","type":"journal_article","language":[{"iso":"eng"}],"volume":36,"article_processing_charge":"No","intvolume":"        36","publisher":"Cell Press","date_created":"2018-12-11T11:49:16Z","oa_version":"None","date_published":"2016-01-12T00:00:00Z","extern":"1","publist_id":"6510","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","day":"12","citation":{"chicago":"Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford. “Emergence of an Apical Epithelial Cell Surface In Vivo.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2015.12.013\">https://doi.org/10.1016/j.devcel.2015.12.013</a>.","mla":"Sedzinski, Jakub, et al. “Emergence of an Apical Epithelial Cell Surface In Vivo.” <i>Developmental Cell</i>, vol. 36, no. 1, Cell Press, 2016, pp. 24–35, doi:<a href=\"https://doi.org/10.1016/j.devcel.2015.12.013\">10.1016/j.devcel.2015.12.013</a>.","ama":"Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. Emergence of an Apical Epithelial Cell Surface In Vivo. <i>Developmental Cell</i>. 2016;36(1):24-35. doi:<a href=\"https://doi.org/10.1016/j.devcel.2015.12.013\">10.1016/j.devcel.2015.12.013</a>","ista":"Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2016. Emergence of an Apical Epithelial Cell Surface In Vivo. Developmental Cell. 36(1), 24–35.","short":"J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Developmental Cell 36 (2016) 24–35.","ieee":"J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “Emergence of an Apical Epithelial Cell Surface In Vivo,” <i>Developmental Cell</i>, vol. 36, no. 1. Cell Press, pp. 24–35, 2016.","apa":"Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., &#38; Wallingford, J. (2016). Emergence of an Apical Epithelial Cell Surface In Vivo. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2015.12.013\">https://doi.org/10.1016/j.devcel.2015.12.013</a>"}},{"publisher":"Springer Nature ","intvolume":"       538","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/","open_access":"1"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"date_created":"2021-06-04T11:34:55Z","scopus_import":"1","date_published":"2016-10-27T00:00:00Z","extern":"1","external_id":{"pmid":["27760113"]},"date_updated":"2021-12-14T07:55:30Z","publication":"Nature","page":"533-536","article_type":"letter_note","oa":1,"year":"2016","article_processing_charge":"No","volume":538,"pmid":1,"month":"10","citation":{"chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536."},"day":"27","oa_version":"Submitted Version","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","status":"public","_id":"9456","title":"Mechanism for DNA transposons to generate introns on genomic scales","author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"last_name":"Roy","full_name":"Roy, Scott W.","first_name":"Scott W."}],"doi":"10.1038/nature20110","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"issue":"7626"},{"pmid":1,"month":"12","day":"27","citation":{"apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>."},"oa_version":"Published Version","volume":113,"article_processing_charge":"No","_id":"9473","author":[{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"first_name":"Toby","last_name":"Buttress","full_name":"Buttress, Toby"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","doi":"10.1073/pnas.1619074114","issue":"52","abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"scopus_import":"1","date_created":"2021-06-07T06:21:39Z","date_published":"2016-12-27T00:00:00Z","extern":"1","external_id":{"pmid":["27956643"]},"intvolume":"       113","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619074114","open_access":"1"}],"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","oa":1,"year":"2016","date_updated":"2023-05-08T11:00:40Z","publication":"Proceedings of the National Academy of Sciences","article_type":"original","page":"15132-15137"},{"date_updated":"2023-05-08T11:00:07Z","publication":"Proceedings of the National Academy of Sciences","page":"15138-15143","article_type":"original","oa":1,"keyword":["Multidisciplinary"],"year":"2016","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619047114"}],"intvolume":"       113","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"date_created":"2021-06-07T07:10:59Z","scopus_import":"1","external_id":{"pmid":["27956642"]},"extern":"1","date_published":"2016-12-27T00:00:00Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","publication_status":"published","_id":"9477","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","author":[{"full_name":"Park, Kyunghyuk","last_name":"Park","first_name":"Kyunghyuk"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jin-Sup","full_name":"Park, Jin-Sup","last_name":"Park"},{"first_name":"Youbong","full_name":"Hyun, Youbong","last_name":"Hyun"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Yeonhee","full_name":"Choi, Yeonhee","last_name":"Choi"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"}],"doi":"10.1073/pnas.1619047114","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"issue":"52","volume":113,"article_processing_charge":"No","pmid":1,"month":"12","citation":{"mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>"},"day":"27","oa_version":"Published Version"},{"publisher":"Neural Information Processing Systems","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"intvolume":"        29","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6469","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:49:21Z","scopus_import":1,"date_updated":"2021-01-12T08:22:08Z","page":"4285 - 4293","year":"2016","alternative_title":["Advances in Neural Information Processing Systems"],"volume":29,"citation":{"mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.","apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293."},"day":"01","month":"01","oa_version":"None","conference":{"end_date":"2016-12-10","location":"Barcelona, Spaine","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"status":"public","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","publication_status":"published","ec_funded":1,"title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","author":[{"last_name":"Monk","full_name":"Monk, Travis","first_name":"Travis"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","full_name":"Savin, Cristina","last_name":"Savin"},{"full_name":"Lücke, Jörg","last_name":"Lücke","first_name":"Jörg"}],"_id":"948","abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}]},{"publication_identifier":{"eissn":["1469-2163"],"issn":["0963-5483"]},"publication_status":"published","status":"public","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","author":[{"full_name":"Krivelevich, Michael","last_name":"Krivelevich","first_name":"Michael"},{"full_name":"Kwan, Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"}],"_id":"9591","abstract":[{"lang":"eng","text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight."}],"issue":"6","doi":"10.1017/s0963548316000079","arxiv":1,"volume":25,"article_processing_charge":"No","citation":{"ista":"Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing. 25(6), 909–927.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing 25 (2016) 909–927.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Combinatorics, Probability and Computing</i>. 2016;25(6):909-927. doi:<a href=\"https://doi.org/10.1017/s0963548316000079\">10.1017/s0963548316000079</a>","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2016). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Combinatorics, Probability and Computing</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0963548316000079\">https://doi.org/10.1017/s0963548316000079</a>","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Combinatorics, Probability and Computing</i>, vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Combinatorics, Probability and Computing</i>, vol. 25, no. 6, Cambridge University Press, 2016, pp. 909–27, doi:<a href=\"https://doi.org/10.1017/s0963548316000079\">10.1017/s0963548316000079</a>.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Combinatorics, Probability and Computing</i>. Cambridge University Press, 2016. <a href=\"https://doi.org/10.1017/s0963548316000079\">https://doi.org/10.1017/s0963548316000079</a>."},"day":"01","month":"11","oa_version":"Preprint","publication":"Combinatorics, Probability and Computing","date_updated":"2023-02-23T14:02:07Z","page":"909-927","article_type":"original","oa":1,"year":"2016","publisher":"Cambridge University Press","intvolume":"        25","main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","date_published":"2016-11-01T00:00:00Z","external_id":{"arxiv":["1501.04816"]},"date_created":"2021-06-22T12:35:13Z","scopus_import":"1"},{"citation":{"mla":"Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10, doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>.","chicago":"Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal DNA Genes.” <i>Nature</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>.","ista":"Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature. 540(7634), 607–610.","ama":"Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. 2016;540(7634):607-610. doi:<a href=\"https://doi.org/10.1038/nature20561\">10.1038/nature20561</a>","short":"S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C. Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610.","apa":"Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A., … Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal DNA genes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature20561\">https://doi.org/10.1038/nature20561</a>","ieee":"S. Neyer <i>et al.</i>, “Structure of RNA polymerase I transcribing ribosomal DNA genes,” <i>Nature</i>, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016."},"day":"22","pmid":1,"month":"12","oa_version":"None","article_processing_charge":"No","volume":540,"title":"Structure of RNA polymerase I transcribing ribosomal DNA genes","author":[{"last_name":"Neyer","full_name":"Neyer, Simon","first_name":"Simon"},{"first_name":"Michael","last_name":"Kunz","full_name":"Kunz, Michael"},{"last_name":"Geiss","full_name":"Geiss, Christian","first_name":"Christian"},{"first_name":"Merle","full_name":"Hantsche, Merle","last_name":"Hantsche"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"first_name":"Anja","last_name":"Seybert","full_name":"Seybert, Anja"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"},{"first_name":"Margot P.","last_name":"Scheffer","full_name":"Scheffer, Margot P."},{"first_name":"Patrick","full_name":"Cramer, Patrick","last_name":"Cramer"},{"first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S.","last_name":"Frangakis"}],"_id":"9654","abstract":[{"text":"RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.","lang":"eng"}],"issue":"7634","doi":"10.1038/nature20561","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2016-12-22T00:00:00Z","external_id":{"pmid":["27842382"]},"extern":"1","date_created":"2021-07-14T09:04:24Z","scopus_import":"1","publisher":"Springer Nature","intvolume":"       540","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","year":"2016","publication":"Nature","date_updated":"2021-07-22T09:22:20Z","page":"607-610","article_type":"letter_note"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","external_id":{"pmid":["27203358"]},"date_published":"2016-06-16T00:00:00Z","date_created":"2021-07-19T08:57:32Z","scopus_import":"1","publisher":"American Chemical Society","intvolume":"         7","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","year":"2016","publication":"The Journal of Physical Chemistry Letters","date_updated":"2023-02-23T14:04:49Z","page":"2210-2215","article_type":"letter_note","citation":{"short":"B. Cheng, J. Behler, M. Ceriotti, The Journal of Physical Chemistry Letters 7 (2016) 2210–2215.","ista":"Cheng B, Behler J, Ceriotti M. 2016. Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. The Journal of Physical Chemistry Letters. 7(12), 2210–2215.","ama":"Cheng B, Behler J, Ceriotti M. Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. <i>The Journal of Physical Chemistry Letters</i>. 2016;7(12):2210-2215. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">10.1021/acs.jpclett.6b00729</a>","apa":"Cheng, B., Behler, J., &#38; Ceriotti, M. (2016). Nuclear quantum effects in water at the triple point: Using theory as a link between experiments. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">https://doi.org/10.1021/acs.jpclett.6b00729</a>","ieee":"B. Cheng, J. Behler, and M. Ceriotti, “Nuclear quantum effects in water at the triple point: Using theory as a link between experiments,” <i>The Journal of Physical Chemistry Letters</i>, vol. 7, no. 12. American Chemical Society, pp. 2210–2215, 2016.","mla":"Cheng, Bingqing, et al. “Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link between Experiments.” <i>The Journal of Physical Chemistry Letters</i>, vol. 7, no. 12, American Chemical Society, 2016, pp. 2210–15, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">10.1021/acs.jpclett.6b00729</a>.","chicago":"Cheng, Bingqing, Jörg Behler, and Michele Ceriotti. “Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link between Experiments.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.jpclett.6b00729\">https://doi.org/10.1021/acs.jpclett.6b00729</a>."},"day":"16","month":"06","pmid":1,"oa_version":"None","article_processing_charge":"No","volume":7,"title":"Nuclear quantum effects in water at the triple point: Using theory as a link between experiments","author":[{"last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"first_name":"Jörg","full_name":"Behler, Jörg","last_name":"Behler"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"_id":"9681","abstract":[{"text":"One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell–Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.","lang":"eng"}],"issue":"12","doi":"10.1021/acs.jpclett.6b00729","publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","status":"public"},{"citation":{"apa":"Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse, M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>","ieee":"D. Aasen <i>et al.</i>, “Milestones toward Majorana-based quantum computing,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","ista":"Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based quantum computing. Physical Review X. 6(3), 031016.","short":"D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse, T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6 (2016).","ama":"Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>","mla":"Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>, vol. 6, no. 3, 031016, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>.","chicago":"Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>."},"day":"03","month":"08","ddc":["530"],"file_date_updated":"2019-05-15T14:12:31Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2019-05-15T14:12:31Z","file_name":"2016_PhysRevX_Aasen.pdf","file_size":2142676,"relation":"main_file","creator":"kschuh","file_id":"6458","date_created":"2019-05-15T14:12:31Z"}],"has_accepted_license":"1","volume":6,"title":"Milestones toward Majorana-based quantum computing","author":[{"first_name":"David","last_name":"Aasen","full_name":"Aasen, David"},{"full_name":"Hell, Michael","last_name":"Hell","first_name":"Michael"},{"last_name":"Mishmash","full_name":"Mishmash, Ryan","first_name":"Ryan"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"full_name":"Danon, Jeroen","last_name":"Danon","first_name":"Jeroen"},{"full_name":"Leijnse, Martin","last_name":"Leijnse","first_name":"Martin"},{"last_name":"Jespersen","full_name":"Jespersen, Thomas","first_name":"Thomas"},{"first_name":"Joshua","full_name":"Folk, Joshua","last_name":"Folk"},{"full_name":"Marcs, Charles","last_name":"Marcs","first_name":"Charles"},{"full_name":"Flensberg, Karsten","last_name":"Flensberg","first_name":"Karsten"},{"full_name":"Alicea, Jason","last_name":"Alicea","first_name":"Jason"}],"_id":"100","abstract":[{"text":"We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system\\'s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well.","lang":"eng"}],"issue":"3","doi":"10.1103/PhysRevX.6.031016","publication_status":"published","status":"public","acknowledgement":"We acknowledge support from Microsoft Research, the National Science Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation (J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish Research Council (M. L.); The Danish National Research Foundation, and the Villum Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences, and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-1066293 (R. V. M.).","publist_id":"7954","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-08-03T00:00:00Z","extern":"1","date_created":"2018-12-11T11:44:37Z","publisher":"American Physical Society","intvolume":"         6","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"year":"2016","publication":"Physical Review X","date_updated":"2021-01-12T06:47:33Z","article_number":"031016"},{"year":"2016","issue":"10","abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"doi":"10.1021/acssynbio.6b00013","author":[{"last_name":"Gnügge","full_name":"Gnügge, Robert","first_name":"Robert"},{"full_name":"Dharmarajan, Lekshmi","last_name":"Dharmarajan","first_name":"Lekshmi"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz","last_name":"Lang"},{"last_name":"Stelling","full_name":"Stelling, Jörg","first_name":"Jörg"}],"title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","_id":"1008","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","status":"public","publication_status":"published","page":"1098 - 1107","publication":"ACS Synthetic Biology","date_updated":"2021-01-12T06:47:37Z","date_published":"2016-05-05T00:00:00Z","date_created":"2018-12-11T11:49:40Z","oa_version":"None","department":[{"_id":"CaGu"}],"day":"05","citation":{"ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>."},"publist_id":"6390","month":"05","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","volume":5,"intvolume":"         5","publisher":"American Chemical Society"},{"oa_version":"Submitted Version","month":"03","citation":{"apa":"Albrecht, S. M., Higginbotham, A. P., Jespersen, T., Madsen, M., Kuemmeth, F., Nygård, J., … Marcus, C. (2016). Exponential protection of zero modes in Majorana islands. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>","ieee":"S. M. Albrecht <i>et al.</i>, “Exponential protection of zero modes in Majorana islands,” <i>Nature</i>, vol. 531, no. 7593. Nature Publishing Group, pp. 206–209, 2016.","ista":"Albrecht SM, Higginbotham AP, Jespersen T, Madsen M, Kuemmeth F, Nygård J, Krogstrup P, Marcus C. 2016. Exponential protection of zero modes in Majorana islands. Nature. 531(7593), 206–209.","short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","ama":"Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of zero modes in Majorana islands. <i>Nature</i>. 2016;531(7593):206-209. doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>","chicago":"Albrecht, S M, Andrew P Higginbotham, Thomas Jespersen, Morten Madsen, Ferdinand Kuemmeth, Jesper Nygård, Peter Krogstrup, and Charles Marcus. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>.","mla":"Albrecht, S. M., et al. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>, vol. 531, no. 7593, Nature Publishing Group, 2016, pp. 206–09, doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>."},"day":"10","volume":531,"arxiv":1,"doi":"10.1038/nature17162","abstract":[{"lang":"eng","text":"Majorana zero modes are quasiparticle excitations in condensed matter systems that have been proposed as building blocks of fault-tolerant quantum computers. They are expected to exhibit non-Abelian particle statistics, in contrast to the usual statistics of fermions and bosons, enabling quantum operations to be performed by braiding isolated modes around one another. Quantum braiding operations are topologically protected insofar as these modes are pinned near zero energy, with the departure from zero expected to be exponentially small as the modes become spatially separated. Following theoretical proposals, several experiments have identified signatures of Majorana modes in nanowires with proximity-induced superconductivity and atomic chains, with small amounts of mode splitting potentially explained by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy Majorana modes. We observe exponential suppression of energy splitting with increasing wire length. For short devices of a few hundred nanometres, sub-gap state energies oscillate as the magnetic field is varied, as is expected for hybridized Majorana modes. Splitting decreases by a factor of about ten for each half a micrometre of increased wire length. For devices longer than about one micrometre, transport in strong magnetic fields occurs through a zero-energy state that is energetically isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance peaks, consistent with teleportation via Majorana modes. Our results help to explain the trivial-to-topological transition in finite systems and to quantify the scaling of topological protection with end-mode separation."}],"issue":"7593","_id":"101","title":"Exponential protection of zero modes in Majorana islands","author":[{"full_name":"Albrecht, S M","last_name":"Albrecht","first_name":"S M"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"first_name":"Thomas","last_name":"Jespersen","full_name":"Jespersen, Thomas"},{"first_name":"Morten","last_name":"Madsen","full_name":"Madsen, Morten"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"},{"last_name":"Nygård","full_name":"Nygård, Jesper","first_name":"Jesper"},{"last_name":"Krogstrup","full_name":"Krogstrup, Peter","first_name":"Peter"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"acknowledgement":"This research was supported by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation and the European Commission. C.M.M. acknowledges support from the Villum Foundation.","status":"public","publication_status":"published","date_created":"2018-12-11T11:44:38Z","external_id":{"arxiv":["1603.03217"]},"extern":"1","date_published":"2016-03-10T00:00:00Z","publist_id":"7953","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Nature Publishing Group","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.03217"}],"intvolume":"       531","year":"2016","oa":1,"page":"206 - 209","date_updated":"2021-01-12T06:47:37Z","publication":"Nature"},{"date_updated":"2021-01-12T06:47:42Z","publication":"Physical Review B","article_number":"245404","oa":1,"year":"2016","main_file_link":[{"url":"https://arxiv.org/abs/1601.07908","open_access":"1"}],"intvolume":"        93","publisher":"American Physical Society","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publist_id":"7952","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:38Z","external_id":{"arxiv":["1601.07908"]},"extern":"1","date_published":"2016-06-08T00:00:00Z","publication_status":"published","status":"public","_id":"102","author":[{"first_name":"Ryan","last_name":"Mishmash","full_name":"Mishmash, Ryan"},{"last_name":"Aasen","full_name":"Aasen, David","first_name":"David"},{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alicea, Jason","last_name":"Alicea","first_name":"Jason"}],"title":"Approaching a topological phase transition in Majorana nanowires","doi":"10.1103/PhysRevB.93.245404","issue":"24","abstract":[{"text":"Recent experiments have produced mounting evidence of Majorana zero modes in nanowire-superconductor hybrids. Signatures of an expected topological phase transition accompanying the onset of these modes nevertheless remain elusive. We investigate a fundamental question concerning this issue: Do well-formed Majorana modes necessarily entail a sharp phase transition in these setups? Assuming reasonable parameters, we argue that finite-size effects can dramatically smooth this putative transition into a crossover, even in systems large enough to support well-localized Majorana modes. We propose overcoming such finite-size effects by examining the behavior of low-lying excited states through tunneling spectroscopy. In particular, the excited-state energies exhibit characteristic field and density dependence, and scaling with system size, that expose an approaching topological phase transition. We suggest several experiments for extracting the predicted behavior. As a useful byproduct, the protocols also allow one to measure the wire's spin-orbit coupling directly in its superconducting environment.","lang":"eng"}],"arxiv":1,"volume":93,"month":"06","day":"08","citation":{"chicago":"Mishmash, Ryan, David Aasen, Andrew P Higginbotham, and Jason Alicea. “Approaching a Topological Phase Transition in Majorana Nanowires.” <i>Physical Review B</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">https://doi.org/10.1103/PhysRevB.93.245404</a>.","mla":"Mishmash, Ryan, et al. “Approaching a Topological Phase Transition in Majorana Nanowires.” <i>Physical Review B</i>, vol. 93, no. 24, 245404, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>.","ama":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. 2016;93(24). doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>","ista":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.","short":"R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93 (2016).","ieee":"R. Mishmash, D. Aasen, A. P. Higginbotham, and J. Alicea, “Approaching a topological phase transition in Majorana nanowires,” <i>Physical Review B</i>, vol. 93, no. 24. American Physical Society, 2016.","apa":"Mishmash, R., Aasen, D., Higginbotham, A. P., &#38; Alicea, J. (2016). Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">https://doi.org/10.1103/PhysRevB.93.245404</a>"},"oa_version":"Preprint"}]