[{"month":"05","publication_identifier":{"issn":["1047-8477"]},"doi":"10.1016/j.jsb.2014.03.018","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["24698954"]},"quality_controlled":"1","file_date_updated":"2021-07-22T08:06:34Z","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","extern":"1","author":[{"full_name":"Perkovic, Mario","first_name":"Mario","last_name":"Perkovic"},{"last_name":"Kunz","first_name":"Michael","full_name":"Kunz, Michael"},{"full_name":"Endesfelder, Ulrike","last_name":"Endesfelder","first_name":"Ulrike"},{"first_name":"Stefanie","last_name":"Bunse","full_name":"Bunse, Stefanie"},{"full_name":"Wigge, Christoph","first_name":"Christoph","last_name":"Wigge"},{"first_name":"Zhou","last_name":"Yu","full_name":"Yu, Zhou"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Scheffer, Margot P.","last_name":"Scheffer","first_name":"Margot P."},{"last_name":"Seybert","first_name":"Anja","full_name":"Seybert, Anja"},{"last_name":"Malkusch","first_name":"Sebastian","full_name":"Malkusch, Sebastian"},{"first_name":"Erin M.","last_name":"Schuman","full_name":"Schuman, Erin M."},{"full_name":"Heilemann, Mike","last_name":"Heilemann","first_name":"Mike"},{"last_name":"Frangakis","first_name":"Achilleas S.","full_name":"Frangakis, Achilleas S."}],"date_created":"2021-07-14T09:05:42Z","date_updated":"2021-07-22T08:26:32Z","volume":186,"year":"2014","pmid":1,"publication_status":"published","publisher":"Elsevier","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2014-05-01T00:00:00Z","publication":"Journal of Structural Biology","citation":{"ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 2014;186(2):205-213. doi:10.1016/j.jsb.2014.03.018","ieee":"M. Perkovic et al., “Correlative light- and electron microscopy with chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213.","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:10.1016/j.jsb.2014.03.018.","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.jsb.2014.03.018."},"article_type":"original","page":"205-213","abstract":[{"text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"relation":"main_file","file_id":"9701","checksum":"a322991b43cdc5935c99db88d285aa3a","success":1,"date_updated":"2021-07-22T08:06:34Z","date_created":"2021-07-22T08:06:34Z","access_level":"open_access","file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","file_size":3454628,"content_type":"application/pdf","creator":"asandaue"}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9655","status":"public","ddc":["570"],"title":"Correlative light- and electron microscopy with chemical tags","intvolume":" 186"},{"scopus_import":"1","month":"06","day":"23","publication_identifier":{"eissn":["1478-6443"],"issn":["1478-6435"]},"article_processing_charge":"No","quality_controlled":"1","article_type":"original","page":"1845-1865","publication":"Philosophical Magazine","citation":{"ieee":"B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” Philosophical Magazine, vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014.","apa":"Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008","ista":"Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.","ama":"Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865. doi:10.1080/14786435.2014.897008","chicago":"Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008.","short":"B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.","mla":"Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor & Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008."},"language":[{"iso":"eng"}],"date_published":"2014-06-23T00:00:00Z","doi":"10.1080/14786435.2014.897008","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings."}],"issue":"16-18","status":"public","title":"Strength of metals under vibrations – dislocation-density-function dynamics simulations","publication_status":"published","publisher":"Taylor & Francis","intvolume":" 95","_id":"9686","year":"2014","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-19T09:27:15Z","date_updated":"2023-02-23T14:04:59Z","oa_version":"None","volume":95,"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"last_name":"Leung","first_name":"H.S.","full_name":"Leung, H.S."},{"full_name":"Ngan, A.H.W.","first_name":"A.H.W.","last_name":"Ngan"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":1,"date_published":"2014-04-25T00:00:00Z","page":"2296 - 2305","article_type":"original","citation":{"ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305.","apa":"Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12440.","mla":"Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305."},"publication":"Evolution","issue":"8","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"7845","relation":"main_file","checksum":"8d459b07e4a11bb5fde92d969184fe48","date_created":"2020-05-14T16:40:31Z","date_updated":"2020-07-14T12:45:28Z","access_level":"open_access","file_name":"2014_Evolution_Lagator.pdf","creator":"dernst","file_size":467254,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 68","ddc":["570"],"status":"public","title":"Role of sex and migration in adaptation to sink environments","_id":"2083","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","language":[{"iso":"eng"}],"doi":"10.1111/evo.12440","quality_controlled":"1","oa":1,"publist_id":"4954","file_date_updated":"2020-07-14T12:45:28Z","volume":68,"date_updated":"2023-02-23T14:06:51Z","date_created":"2018-12-11T11:55:36Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9747"}]},"author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Morgan, Andrew","last_name":"Morgan","first_name":"Andrew"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"department":[{"_id":"CaGu"}],"publisher":"Wiley","publication_status":"published","year":"2014","acknowledgement":"The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work."},{"doi":"10.5061/dryad.s42n1","date_published":"2014-04-17T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s42n1","open_access":"1"}],"oa":1,"citation":{"mla":"Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1"},"month":"04","day":"17","article_processing_charge":"No","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Morgan, Andrew","first_name":"Andrew","last_name":"Morgan"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2083"}]},"date_updated":"2023-02-23T10:27:31Z","date_created":"2021-07-28T15:32:55Z","oa_version":"Published Version","year":"2014","_id":"9747","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Role of sex and migration in adaptation to sink environments","status":"public","publisher":"Dryad","department":[{"_id":"CaGu"}],"abstract":[{"lang":"eng","text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment."}],"type":"research_data_reference"},{"extern":1,"abstract":[{"lang":"eng","text":"We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems."}],"issue":"14","publist_id":"6421","type":"journal_article","date_updated":"2021-01-12T08:22:22Z","date_created":"2018-12-11T11:49:30Z","volume":113,"author":[{"full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Knap, Michael J","first_name":"Michael","last_name":"Knap"},{"last_name":"Gopalakrishnan","first_name":"Sarang","full_name":"Gopalakrishnan, Sarang"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Norman","last_name":"Yao","full_name":"Yao, Norman Y"},{"full_name":"Laumann, Chris R","first_name":"Chris","last_name":"Laumann"},{"full_name":"Abanin, Dmitry A","first_name":"Dmitry","last_name":"Abanin"},{"last_name":"Lukin","first_name":"Mikhail","full_name":"Lukin, Mikhail D"},{"last_name":"Demler","first_name":"Eugene","full_name":"Demler, Eugene A"}],"publication_status":"published","title":"Interferometric probes of many-body localization","status":"public","publisher":"American Physical Society","intvolume":" 113","acknowledgement":"We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.\n\nM. S., M. K., and S. G. contributed equally to this work.","_id":"977","year":"2014","day":"03","month":"10","date_published":"2014-10-03T00:00:00Z","doi":"10.1103/PhysRevLett.113.147204","quality_controlled":0,"publication":"Physical Review Letters","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.0693"}],"citation":{"ama":"Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204","ista":"Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14).","ieee":"M. Serbyn et al., “Interferometric probes of many-body localization,” Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014.","apa":"Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204","mla":"Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.147204.","short":"M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014).","chicago":"Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204."}},{"type":"journal_article","issue":"17","publist_id":"6420","abstract":[{"text":"Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.","lang":"eng"}],"extern":1,"acknowledgement":"Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.).","_id":"980","year":"2014","publisher":"American Physical Society","intvolume":" 90","publication_status":"published","status":"public","title":"Quantum quenches in the many-body localized phase","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry A"}],"volume":90,"date_created":"2018-12-11T11:49:31Z","date_updated":"2021-01-12T08:22:24Z","day":"06","month":"11","citation":{"chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302.","mla":"Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","ista":"Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17. American Physical Society, 2014.","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302","ama":"Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 2014;90(17). doi:10.1103/PhysRevB.90.174302"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.4105"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","quality_controlled":0,"date_published":"2014-11-06T00:00:00Z","doi":"10.1103/PhysRevB.90.174302"},{"month":"05","doi":"10.1021/nl501242b","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.2093"}],"external_id":{"arxiv":["1403.2093"]},"oa":1,"quality_controlled":"1","publist_id":"7956","extern":"1","author":[{"first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"first_name":"Thorvald","last_name":"Larsen","full_name":"Larsen, Thorvald"},{"last_name":"Yao","first_name":"Jun","full_name":"Yao, Jun"},{"full_name":"Yan, Hao","last_name":"Yan","first_name":"Hao"},{"full_name":"Lieber, Charles","first_name":"Charles","last_name":"Lieber"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"}],"volume":14,"date_updated":"2021-01-12T08:22:24Z","date_created":"2018-12-11T11:44:37Z","acknowledgement":"Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged.","year":"2014","publisher":"American Chemical Society","publication_status":"published","day":"05","date_published":"2014-05-05T00:00:00Z","citation":{"ama":"Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b","ista":"Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586.","ieee":"A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014.","apa":"Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., & Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b","mla":"Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:10.1021/nl501242b.","short":"A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586.","chicago":"Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b."},"publication":"Nano Letters","page":"3582 - 3586","issue":"6","abstract":[{"text":"Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"98","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 14","title":"Hole spin coherence in a Ge/Si heterostructure nanowire","status":"public"},{"acknowledgement":"This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC).","year":"2014","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","author":[{"full_name":"Wolf, Stephan","first_name":"Stephan","last_name":"Wolf"},{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Lim","first_name":"Ka","full_name":"Lim, Ka"},{"full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"},{"last_name":"Clark","first_name":"Suzanne","full_name":"Clark, Suzanne"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"},{"first_name":"Juliet","last_name":"Osborne","full_name":"Osborne, Juliet"}],"related_material":{"record":[{"id":"9888","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:55:37Z","date_updated":"2023-02-23T14:11:56Z","volume":9,"article_number":"e103989","file_date_updated":"2020-07-14T12:45:28Z","publist_id":"4949","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0103989","language":[{"iso":"eng"}],"month":"08","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2086","title":"So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees","status":"public","ddc":["570"],"intvolume":" 9","pubrep_id":"437","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5042","date_updated":"2020-07-14T12:45:28Z","date_created":"2018-12-12T10:13:55Z","checksum":"2fc62c6739eada4bddf026afbae669db","file_name":"IST-2016-437-v1+1_journal.pone.0103989.pdf","access_level":"open_access","file_size":1013386,"content_type":"application/pdf","creator":"system"}],"type":"journal_article","abstract":[{"text":"Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.","lang":"eng"}],"issue":"8","publication":"PLoS One","citation":{"mla":"Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8, e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS One 9 (2014).","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.","ama":"Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8). doi:10.1371/journal.pone.0103989","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 9(8), e103989.","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989","ieee":"S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8. Public Library of Science, 2014."},"date_published":"2014-08-06T00:00:00Z","scopus_import":1,"day":"06","has_accepted_license":"1"},{"article_processing_charge":"No","month":"08","day":"06","citation":{"ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, 10.1371/journal.pone.0103989.s003.","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989.s003","ieee":"S. Wolf et al., “Supporting information.” Public Library of Science, 2014.","ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:10.1371/journal.pone.0103989.s003","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.s003.","mla":"Wolf, Stephan, et al. Supporting Information. Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.s003.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014)."},"doi":"10.1371/journal.pone.0103989.s003","type":"research_data_reference","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"status":"public","title":"Supporting information","year":"2014","_id":"9888","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-11T14:17:53Z","date_updated":"2023-02-23T10:27:38Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2086"}]},"author":[{"full_name":"Wolf, Stephan","last_name":"Wolf","first_name":"Stephan"},{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"full_name":"Lim, Ka","first_name":"Ka","last_name":"Lim"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull","full_name":"Pull, Christopher"},{"full_name":"Clark, Suzanne","first_name":"Suzanne","last_name":"Clark"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"},{"last_name":"Osborne","first_name":"Juliet","full_name":"Osborne, Juliet"}]},{"page":"3016 - 3025","quality_controlled":0,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.","mla":"Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.","chicago":"Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242.","ama":"Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242","ieee":"V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.","apa":"Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu242","ista":"Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025."},"publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msu242","date_published":"2014-11-01T00:00:00Z","day":"01","month":"11","publisher":"Oxford University Press","intvolume":" 31","status":"public","title":"Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity","publication_status":"published","year":"2014","_id":"845","acknowledgement":"The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan.","volume":31,"date_updated":"2021-01-12T08:19:21Z","date_created":"2018-12-11T11:48:48Z","author":[{"first_name":"Vladimir","last_name":"Seplyarskiy","full_name":"Seplyarskiy, Vladimir B"},{"first_name":"Maria","last_name":"Logacheva","full_name":"Logacheva, Maria D"},{"full_name":"Penin, Aleksey A","first_name":"Aleksey","last_name":"Penin"},{"full_name":"Baranová, Maria A","first_name":"Maria","last_name":"Baranová"},{"last_name":"Leushkin","first_name":"Evgeny","full_name":"Leushkin, Evgeny V"},{"last_name":"Demidenko","first_name":"Natalia","full_name":"Demidenko, Natalia V"},{"last_name":"Klepikova","first_name":"Anna","full_name":"Klepikova, Anna V"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"},{"full_name":"James, Timothy Y","first_name":"Timothy","last_name":"James"}],"type":"journal_article","extern":1,"issue":"11","publist_id":"6801","abstract":[{"text":"Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.","lang":"eng"}]},{"month":"06","day":"01","publication":"Current Opinion in Structural Biology","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ieee":"D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26, no. 1. Elsevier, pp. 104–112, 2014.","apa":"Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective of compensatory evolution. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2014.05.004","ista":"Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.","ama":"Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004","chicago":"Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.","short":"D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112.","mla":"Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004."},"quality_controlled":0,"page":"104 - 112","doi":"10.1016/j.sbi.2014.05.004","date_published":"2014-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution."}],"publist_id":"6756","issue":"1","extern":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"892","acknowledgement":"The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.\n","year":"2014","title":"A structural perspective of compensatory evolution","publication_status":"published","status":"public","intvolume":" 26","publisher":"Elsevier","author":[{"last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry N"},{"full_name":"Finkelstein, Alexei V","last_name":"Finkelstein","first_name":"Alexei"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"date_created":"2018-12-11T11:49:03Z","date_updated":"2021-01-12T08:21:21Z","volume":26},{"extern":"1","article_number":"1784","author":[{"full_name":"Takagi, Daisuke","first_name":"Daisuke","last_name":"Takagi"},{"first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"},{"first_name":"Adam B.","last_name":"Braunschweig","full_name":"Braunschweig, Adam B."},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"}],"volume":10,"date_created":"2021-02-01T13:43:31Z","date_updated":"2023-02-23T13:47:35Z","pmid":1,"year":"2014","publisher":"Royal Society of Chemistry ","publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"03","doi":"10.1039/c3sm52815d","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.5662"}],"external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"oa":1,"quality_controlled":"1","issue":"11","abstract":[{"lang":"eng","text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter."}],"type":"journal_article","oa_version":"Preprint","_id":"9050","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 10","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","status":"public","article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["General Chemistry","Condensed Matter Physics"],"date_published":"2014-03-21T00:00:00Z","citation":{"ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter, vol. 10, no. 11. Royal Society of Chemistry , 2014.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.","mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:10.1039/c3sm52815d.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014)."},"publication":"Soft Matter","article_type":"original"},{"status":"public","title":"Light-activated self-propelled colloids","intvolume":" 372","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9166","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles."}],"issue":"2029","article_type":"original","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.","short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin, P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2013.0372","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029. The Royal Society, 2014.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372"},"date_published":"2014-11-28T00:00:00Z","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"scopus_import":"1","day":"28","article_processing_charge":"No","publication_status":"published","publisher":"The Royal Society","year":"2014","pmid":1,"date_created":"2021-02-18T14:31:11Z","date_updated":"2021-02-22T10:44:16Z","volume":372,"author":[{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"},{"full_name":"Sacanna, S.","first_name":"S.","last_name":"Sacanna"},{"full_name":"Kim, S.-H.","last_name":"Kim","first_name":"S.-H."},{"full_name":"Yi, G.-R.","last_name":"Yi","first_name":"G.-R."},{"full_name":"Pine, D. J.","last_name":"Pine","first_name":"D. J."},{"full_name":"Chaikin, P. M.","last_name":"Chaikin","first_name":"P. M."}],"article_number":"20130372","extern":"1","quality_controlled":"1","external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1098/rsta.2013.0372","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1098/rsta.2013.0372","month":"11","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]}},{"author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Prost, Jacques","first_name":"Jacques","last_name":"Prost"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"}],"oa_version":"None","volume":11,"date_updated":"2021-01-12T08:21:57Z","date_created":"2018-12-11T11:49:14Z","year":"2014","_id":"926","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","intvolume":" 11","publisher":"Royal Society of London","status":"public","title":"Growth homeostatic regulation and stem cell dynamics in tissues","publication_status":"published","issue":"93","publist_id":"6516","abstract":[{"text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.","lang":"eng"}],"extern":"1","type":"journal_article","date_published":"2014-04-06T00:00:00Z","doi":"10.1098/rsif.2013.0895","language":[{"iso":"eng"}],"citation":{"chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895.","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895"},"publication":"Journal of the Royal Society Interface","article_processing_charge":"No","month":"04","day":"06"},{"extern":"1","publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Elsevier","year":"2014","pmid":1,"date_updated":"2021-12-14T08:22:36Z","date_created":"2021-06-04T12:00:16Z","volume":156,"author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"}],"month":"03","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"external_id":{"pmid":["24630728"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2014.01.029","type":"journal_article","abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"issue":"6","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","status":"public","intvolume":" 156","_id":"9458","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","scopus_import":"1","day":"13","article_processing_charge":"No","article_type":"original","page":"1286-1297","publication":"Cell","citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","apa":"Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029"},"date_published":"2014-03-13T00:00:00Z"},{"issue":"45","abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 111","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","status":"public","_id":"9479","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2014-11-11T00:00:00Z","page":"16166-16171","article_type":"original","citation":{"ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111","ieee":"Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” Proceedings of the National Academy of Sciences, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1418564111","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111."},"publication":"Proceedings of the National Academy of Sciences","extern":"1","volume":111,"date_updated":"2021-12-14T08:23:26Z","date_created":"2021-06-07T07:23:43Z","author":[{"full_name":"Mérai, Zsuzsanna","first_name":"Zsuzsanna","last_name":"Mérai"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar","first_name":"Marcelina"},{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"first_name":"Lucyna","last_name":"Ślusarz","full_name":"Ślusarz, Lucyna"},{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"last_name":"Tamaru","first_name":"Hisashi","full_name":"Tamaru, Hisashi"}],"publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"year":"2014","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1418564111","quality_controlled":"1","oa":1,"external_id":{"pmid":["25344531"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}]},{"date_published":"2014-12-28T00:00:00Z","citation":{"chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4904293.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing, 2014.","apa":"Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4904293","ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293"},"publication":"The Journal of Chemical Physics","article_type":"original","article_processing_charge":"No","day":"28","scopus_import":"1","oa_version":"Preprint","_id":"9662","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 141","title":"Direct path integral estimators for isotope fractionation ratios","status":"public","issue":"24","abstract":[{"lang":"eng","text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons."}],"type":"journal_article","doi":"10.1063/1.4904293","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["25554138"],"arxiv":["1412.1308"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1308"}],"quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"12","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"volume":141,"date_updated":"2021-08-09T12:32:24Z","date_created":"2021-07-15T09:22:49Z","pmid":1,"year":"2014","publisher":"AIP Publishing","publication_status":"published","extern":"1","article_number":"244112"},{"author":[{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"},{"full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth","first_name":"Ferdinand"},{"full_name":"Larsen, Thorvald","last_name":"Larsen","first_name":"Thorvald"},{"last_name":"Fitzpatrick","first_name":"Mattias","full_name":"Fitzpatrick, Mattias"},{"full_name":"Yao, Jun","last_name":"Yao","first_name":"Jun"},{"first_name":"Hao","last_name":"Yan","full_name":"Yan, Hao"},{"full_name":"Lieber, Charles","first_name":"Charles","last_name":"Lieber"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"volume":112,"date_updated":"2021-01-12T08:22:19Z","date_created":"2018-12-11T11:44:36Z","year":"2014","acknowledgement":"Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program.","publisher":"American Physical Society","publication_status":"published","publist_id":"7957","extern":"1","article_number":"216806","doi":"10.1103/PhysRevLett.112.216806","language":[{"iso":"eng"}],"external_id":{"arxiv":["1401.2948"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1401.2948","open_access":"1"}],"quality_controlled":"1","month":"05","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"97","intvolume":" 112","status":"public","title":"Antilocalization of coulomb blockade in a Ge/Si nanowire","issue":"21","abstract":[{"lang":"eng","text":"The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm)."}],"type":"journal_article","date_published":"2014-05-29T00:00:00Z","citation":{"apa":"Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.216806","ieee":"A. P. Higginbotham et al., “Antilocalization of coulomb blockade in a Ge/Si nanowire,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014.","ista":"Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806.","ama":"Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.216806","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.216806.","short":"A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","mla":"Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” APS Physics, Physical Review Letters, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.216806."},"publication":"APS Physics, Physical Review Letters","day":"29"},{"author":[{"full_name":"Lovrics, Anna","last_name":"Lovrics","first_name":"Anna"},{"last_name":"Gao","first_name":"Yu","full_name":"Gao, Yu"},{"last_name":"Juhász","first_name":"Bianka","full_name":"Juhász, Bianka"},{"full_name":"Bock, István","first_name":"István","last_name":"Bock"},{"last_name":"Byrne","first_name":"Helen","full_name":"Byrne, Helen"},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"full_name":"Kovács, Krisztián","last_name":"Kovács","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9722"}]},"date_created":"2018-12-11T11:55:09Z","date_updated":"2023-02-23T14:06:14Z","volume":9,"year":"2014","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:45:24Z","publist_id":"5072","ec_funded":1,"article_number":"e111430","doi":"10.1371/journal.pone.0111430","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"month":"11","pubrep_id":"435","oa_version":"Published Version","file":[{"checksum":"a2289b843f7463eb1233f9ce45e6a943","date_updated":"2020-07-14T12:45:24Z","date_created":"2018-12-12T10:10:58Z","relation":"main_file","file_id":"4850","file_size":829363,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-435-v1+1_journal.pone.0111430.pdf"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2004","ddc":["570"],"title":"Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord","status":"public","intvolume":" 9","abstract":[{"lang":"eng","text":"We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks."}],"issue":"11","type":"journal_article","date_published":"2014-11-14T00:00:00Z","publication":"PLoS One","citation":{"ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., & Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430","ieee":"A. Lovrics et al., “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.","ama":"Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0111430","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.","mla":"Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” PLoS One, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014)."},"day":"14","has_accepted_license":"1","scopus_import":1},{"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","status":"public","publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"year":"2014","_id":"9722","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-26T14:35:00Z","date_updated":"2023-02-23T10:24:07Z","oa_version":"Published Version","author":[{"full_name":"Lovrics, Anna","last_name":"Lovrics","first_name":"Anna"},{"last_name":"Gao","first_name":"Yu","full_name":"Gao, Yu"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"full_name":"Byrne, Helen M.","first_name":"Helen M.","last_name":"Byrne"},{"full_name":"Dinnyés, András","first_name":"András","last_name":"Dinnyés"},{"full_name":"Kovács, Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","first_name":"Krisztián"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2004"}]},"type":"research_data_reference","citation":{"ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, 10.1371/journal.pone.0111430.s006.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., & Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. https://doi.org/10.1371/journal.pone.0111430.s006","ieee":"A. Lovrics et al., “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:10.1371/journal.pone.0111430.s006","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0111430.s006.","mla":"Lovrics, Anna, et al. Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2. Public Library of Science, 2014, doi:10.1371/journal.pone.0111430.s006.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014)."},"doi":"10.1371/journal.pone.0111430.s006","date_published":"2014-11-14T00:00:00Z","month":"11","day":"14","article_processing_charge":"No"}]