[{"article_processing_charge":"No","day":"18","citation":{"chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021.","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021","ieee":"N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021"},"publication":"Nucleic Acids Research","page":"1905-1917","article_type":"original","date_published":"2015-02-18T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9017","intvolume":" 43","status":"public","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","oa_version":"Published Version","publication_identifier":{"issn":["1362-4962","0305-1048"]},"month":"02","external_id":{"pmid":["25618846"]},"quality_controlled":"1","doi":"10.1093/nar/gkv021","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2015","publisher":"Oxford University Press","publication_status":"published","author":[{"full_name":"Richet, Nicolas","first_name":"Nicolas","last_name":"Richet"},{"full_name":"Liu, Danni","first_name":"Danni","last_name":"Liu"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"full_name":"Velours, Christophe","last_name":"Velours","first_name":"Christophe"},{"last_name":"Corpet","first_name":"Armelle","full_name":"Corpet, Armelle"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail","first_name":"May M","full_name":"Bakail, May M"},{"last_name":"Moal-Raisin","first_name":"Gwenaelle","full_name":"Moal-Raisin, Gwenaelle"},{"full_name":"Guerois, Raphael","first_name":"Raphael","last_name":"Guerois"},{"last_name":"Compper","first_name":"Christel","full_name":"Compper, Christel"},{"full_name":"Besle, Arthur","last_name":"Besle","first_name":"Arthur"},{"full_name":"Guichard, Berengère","first_name":"Berengère","last_name":"Guichard"},{"last_name":"Almouzni","first_name":"Genevieve","full_name":"Almouzni, Genevieve"},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"}],"volume":43,"date_updated":"2023-02-23T13:46:50Z","date_created":"2021-01-19T11:01:01Z"},{"article_processing_charge":"No","day":"05","month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.applthermaleng.2014.10.009","date_published":"2015-02-05T00:00:00Z","page":"1 - 8","citation":{"short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.","chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009.","ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8."},"publication":"Applied Thermal Engineering","extern":"1","publist_id":"6514","abstract":[{"lang":"eng","text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper."}],"type":"journal_article","oa_version":"None","volume":76,"date_updated":"2021-01-12T08:21:56Z","date_created":"2018-12-11T11:49:13Z","author":[{"first_name":"Riadh","last_name":"Boubaker","full_name":"Boubaker, Riadh"},{"full_name":"Platel, Vincent","first_name":"Vincent","last_name":"Platel"},{"first_name":"Alexis","last_name":"Bergès","full_name":"Bergès, Alexis"},{"full_name":"Bancelin, Mathieu","first_name":"Mathieu","last_name":"Bancelin"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"publisher":"Elsevier","intvolume":" 76","status":"public","publication_status":"published","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","year":"2015","_id":"924","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099)."},{"extern":"1","publist_id":"6513","issue":"28","abstract":[{"lang":"eng","text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. "}],"type":"journal_article","volume":112,"oa_version":"None","date_created":"2018-12-11T11:49:15Z","date_updated":"2021-01-12T08:21:59Z","author":[{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"last_name":"Recho","first_name":"Pierre","full_name":"Recho, Pierre"},{"full_name":"Joanny, Jean","first_name":"Jean","last_name":"Joanny"},{"last_name":"Hayashi","first_name":"Shigeo","full_name":"Hayashi, Shigeo"}],"intvolume":" 112","publisher":"National Academy of Sciences","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","status":"public","publication_status":"published","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","_id":"929","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","article_processing_charge":"No","day":"14","month":"07","language":[{"iso":"eng"}],"date_published":"2015-07-14T00:00:00Z","doi":"10.1073/pnas.1504762112","page":"8620 - 8625","citation":{"chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.","apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112"},"publication":"PNAS"},{"date_published":"2015-12-15T00:00:00Z","publication":"PNAS","citation":{"chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112"},"page":"15314 - 15319","day":"15","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"933","title":"Physics of active jamming during collective cellular motion in a monolayer","status":"public","intvolume":" 112","abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"issue":"50","type":"journal_article","doi":"10.1073/pnas.1510973112","language":[{"iso":"eng"}],"external_id":{"pmid":["26627719"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf"}],"quality_controlled":"1","month":"12","author":[{"last_name":"García","first_name":"Simón","full_name":"García, Simón"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"first_name":"Pascal","last_name":"Silberzan","full_name":"Silberzan, Pascal"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"date_updated":"2021-01-12T08:22:01Z","date_created":"2018-12-11T11:49:16Z","volume":112,"year":"2015","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","publist_id":"6511","extern":"1"},{"abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"issue":"24","type":"journal_article","oa_version":"Published Version","file":[{"file_size":1116846,"content_type":"application/pdf","creator":"asandaue","access_level":"open_access","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","checksum":"086a88cfca4677646da26ed960cb02e9","success":1,"date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:55:10Z","relation":"main_file","file_id":"9533"}],"ddc":["570"],"title":"Evolution and function of genomic imprinting in plants","status":"public","intvolume":" 29","_id":"9532","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2015-12-15T00:00:00Z","article_type":"review","page":"2517–2531","publication":"Genes and Development","citation":{"chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115"},"extern":"1","file_date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:56:24Z","date_updated":"2021-12-14T07:58:15Z","volume":29,"author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"publication_status":"published","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"DaZi"}],"year":"2015","pmid":1,"month":"12","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"language":[{"iso":"eng"}],"doi":"10.1101/gad.269902.115","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["26680300"]}},{"publication":"Modelling and Simulation in Materials Science and Engineering","citation":{"ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015.","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001.","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001."},"quality_controlled":"1","article_type":"original","doi":"10.1088/0965-0393/23/3/035001","date_published":"2015-04-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","month":"04","day":"01","article_processing_charge":"No","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9684","year":"2015","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","status":"public","publication_status":"published","intvolume":" 23","publisher":"IOP Publishing","author":[{"last_name":"Leung","first_name":"P S S","full_name":"Leung, P S S"},{"first_name":"H S","last_name":"Leung","full_name":"Leung, H S"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Ngan, A H W","first_name":"A H W","last_name":"Ngan"}],"date_created":"2021-07-19T09:11:12Z","date_updated":"2023-02-23T14:04:54Z","oa_version":"None","volume":23,"article_number":"035001","type":"journal_article","abstract":[{"lang":"eng","text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept."}],"issue":"3","extern":"1"},{"scopus_import":1,"has_accepted_license":"1","day":"23","citation":{"chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541"},"publication":"PLoS Computational Biology","date_published":"2015-10-23T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.","lang":"eng"}],"_id":"1566","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","status":"public","ddc":["570"],"title":"An exploration of the universe of polyglutamine structures","pubrep_id":"478","file":[{"file_size":1412511,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","checksum":"8b67d729be663bfc9af04bfd94459655","date_created":"2018-12-12T10:16:21Z","date_updated":"2020-07-14T12:45:02Z","relation":"main_file","file_id":"5207"}],"oa_version":"Published Version","month":"10","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.pcbi.1004541","language":[{"iso":"eng"}],"article_number":"e1004541","publist_id":"5605","file_date_updated":"2020-07-14T12:45:02Z","year":"2015","acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9714"}]},"author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cieplak","first_name":"Marek","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"volume":11,"date_created":"2018-12-11T11:52:45Z","date_updated":"2023-02-23T14:05:55Z"},{"month":"11","day":"06","article_processing_charge":"No","citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001."},"doi":"10.1371/journal.pgen.1005639.s001","date_published":"2015-11-06T00:00:00Z","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9712","year":"2015","status":"public","title":"Other fitness models for comparison & for interacting TFBSs","publisher":"Public Library of Science","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","first_name":"Murat","last_name":"Tugrul"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1666"}]},"date_updated":"2023-02-23T10:09:08Z","date_created":"2021-07-23T12:00:37Z","oa_version":"Published Version"},{"date_published":"2015-10-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004541.s001","citation":{"short":"À. 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