[{"scopus_import":"1","day":"01","month":"04","article_processing_charge":"No","publication_identifier":{"issn":["0749-6419"]},"publication":"International Journal of Plasticity","citation":{"short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25."},"article_type":"original","page":"1-25","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.ijplas.2014.09.009","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.","lang":"eng"}],"extern":"1","year":"2015","_id":"9673","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","publication_status":"published","publisher":"Elsevier","intvolume":" 67","author":[{"full_name":"Leung, H.S.","last_name":"Leung","first_name":"H.S."},{"last_name":"Leung","first_name":"P.S.S.","full_name":"Leung, P.S.S."},{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"last_name":"Ngan","first_name":"A.H.W.","full_name":"Ngan, A.H.W."}],"date_updated":"2023-02-23T14:04:28Z","date_created":"2021-07-15T14:09:32Z","oa_version":"None","volume":67},{"scopus_import":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102"},"publication":"Physical Review B - Condensed Matter and Materials Physics","date_published":"2015-11-01T00:00:00Z","type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification."}],"intvolume":" 92","status":"public","title":"Solid-liquid interfacial free energy out of equilibrium","_id":"9688","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Preprint","publication_identifier":{"issn":["1098-0121"],"eissn":["1550-235X"]},"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.08668"}],"oa":1,"external_id":{"arxiv":["1511.08668"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.92.180102","article_number":"180102","extern":"1","publisher":"American Physical Society","publication_status":"published","year":"2015","volume":92,"date_created":"2021-07-19T10:07:22Z","date_updated":"2021-08-09T12:38:49Z","author":[{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}]},{"day":"18","month":"11","article_processing_charge":"No","doi":"10.1371/journal.pbio.1002299.s001","date_published":"2015-11-18T00:00:00Z","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.","mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001.","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001"},"type":"research_data_reference","author":[{"full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume"},{"first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta"},{"first_name":"Tugce","last_name":"Batur","full_name":"Batur, Tugce"},{"full_name":"Guvenek, Aysegul","first_name":"Aysegul","last_name":"Guvenek"},{"full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan","first_name":"Dilay Hazal"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1619"}]},"date_created":"2021-07-23T11:53:50Z","date_updated":"2023-02-23T10:07:02Z","oa_version":"Published Version","_id":"9711","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Excel file containing the raw data for all figures","publisher":"Public Library of Science","department":[{"_id":"ToBo"}]},{"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,"external_id":{"pmid":["25646973"]},"quality_controlled":"1","doi":"10.1111/1365-2656.12345","language":[{"iso":"eng"}],"month":"03","year":"2015","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"SyCr"}],"author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"},{"last_name":"Caspar","first_name":"Jesicca","full_name":"Caspar, Jesicca"},{"first_name":"Panagiotis","last_name":"Theodorou","full_name":"Theodorou, Panagiotis"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"related_material":{"record":[{"id":"9720","relation":"research_data","status":"public"}]},"date_updated":"2023-02-23T14:06:09Z","date_created":"2018-12-11T11:54:23Z","volume":84,"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5245","publication":"Journal of Animal Ecology","citation":{"ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345."},"article_type":"original","page":"615 - 624","date_published":"2015-03-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"No","has_accepted_license":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1855","status":"public","ddc":["570"],"title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","intvolume":" 84","pubrep_id":"460","oa_version":"Published Version","file":[{"file_id":"5350","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:18:29Z","checksum":"542a0b9b07e78050a81b35f26f0b82da","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1823045}],"type":"journal_article","abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"issue":"3"},{"type":"journal_article","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"issue":"1669","status":"public","title":"Opposing effects of allogrooming on disease transmission in ant societies","intvolume":" 370","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1830","oa_version":"Submitted Version","scopus_import":"1","day":"26","article_processing_charge":"No","article_type":"original","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","citation":{"ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015)."},"date_published":"2015-05-26T00:00:00Z","publist_id":"5273","ec_funded":1,"publication_status":"published","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"year":"2015","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","pmid":1,"date_updated":"2023-02-23T14:06:12Z","date_created":"2018-12-11T11:54:15Z","volume":370,"author":[{"last_name":"Theis","first_name":"Fabian","full_name":"Theis, Fabian"},{"last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"last_name":"Marr","first_name":"Carsten","full_name":"Marr, Carsten"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9721"}]},"month":"05","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"quality_controlled":"1","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","call_identifier":"FP7"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"},{"name":"Fellowship of Wissenschaftskolleg zu Berlin","_id":"25E24DB2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"external_id":{"pmid":["25870394"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2014.0108"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"_id":"9721","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","status":"public","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","publisher":"Dryad","department":[{"_id":"SyCr"}],"author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"full_name":"Marr, Carsten","last_name":"Marr","first_name":"Carsten"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1830"}]},"date_updated":"2023-02-23T10:16:22Z","date_created":"2021-07-26T09:38:36Z","oa_version":"Published Version","day":"29","month":"12","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.dj2bf"}],"citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf"},"doi":"10.5061/dryad.dj2bf","date_published":"2015-12-29T00:00:00Z"},{"doi":"10.1371/journal.pcbi.1004055.s001","date_published":"2015-03-23T00:00:00Z","citation":{"ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001."},"month":"03","day":"23","article_processing_charge":"No","author":[{"full_name":"Friedlander, Tamar","first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Avraham E.","last_name":"Mayo","full_name":"Mayo, Avraham E."},{"last_name":"Tlusty","first_name":"Tsvi","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1827"}]},"date_updated":"2023-02-23T10:16:13Z","date_created":"2021-07-26T08:35:23Z","oa_version":"Published Version","_id":"9718","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Supporting information text","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"type":"research_data_reference"},{"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.0127657","language":[{"iso":"eng"}],"month":"06","year":"2015","publisher":"Public Library of Science","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9737"}]},"author":[{"full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova"},{"full_name":"Topp, Christopher","first_name":"Christopher","last_name":"Topp"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"volume":10,"date_updated":"2023-02-23T14:06:33Z","date_created":"2018-12-11T11:54:02Z","article_number":"e0127657","publist_id":"5318","file_date_updated":"2020-07-14T12:45:16Z","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657"},"publication":"PLoS One","date_published":"2015-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1793","intvolume":" 10","ddc":["000"],"status":"public","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","pubrep_id":"454","file":[{"relation":"main_file","file_id":"5150","date_created":"2018-12-12T10:15:30Z","date_updated":"2020-07-14T12:45:16Z","checksum":"d20f26461ca575276ad3ed9ce4bfc787","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1850825,"creator":"system"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}]},{"author":[{"last_name":"Symonova","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"full_name":"Topp, Christopher","first_name":"Christopher","last_name":"Topp"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1793"}]},"date_created":"2021-07-28T06:20:13Z","date_updated":"2023-02-23T10:14:42Z","oa_version":"Published Version","_id":"9737","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","status":"public","publisher":"Public Library of Science","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"type":"research_data_reference","doi":"10.1371/journal.pone.0127657.s001","date_published":"2015-06-01T00:00:00Z","citation":{"mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001"},"month":"06","day":"01","article_processing_charge":"No"},{"ec_funded":1,"publist_id":"5278","file_date_updated":"2020-07-14T12:45:17Z","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2015","volume":11,"date_updated":"2023-02-23T14:07:51Z","date_created":"2018-12-11T11:54:14Z","related_material":{"record":[{"id":"9718","status":"public","relation":"research_data"},{"id":"9773","status":"public","relation":"research_data"}]},"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"last_name":"Alon","first_name":"Uri","full_name":"Alon, Uri"}],"month":"03","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","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"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1004055","type":"journal_article","issue":"3","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"intvolume":" 11","status":"public","title":"Evolution of bow-tie architectures in biology","ddc":["576"],"_id":"1827","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":1811647,"creator":"system","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:39Z","checksum":"b8aa66f450ff8de393014b87ec7d2efb","relation":"main_file","file_id":"5161"}],"oa_version":"Published Version","pubrep_id":"452","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"23","citation":{"ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055."},"publication":"PLoS Computational Biology","date_published":"2015-03-23T00:00:00Z"},{"scopus_import":1,"has_accepted_license":"1","day":"18","citation":{"ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907."},"publication":"PLoS One","date_published":"2015-05-18T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"_id":"1809","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","title":"Indirect genetic effects and the dynamics of social interactions","ddc":["570","576"],"status":"public","pubrep_id":"453","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:09:07Z","date_updated":"2020-07-14T12:45:17Z","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_id":"4730","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2748982,"file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","access_level":"open_access"}],"month":"05","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","doi":"10.1371/journal.pone.0126907","language":[{"iso":"eng"}],"publist_id":"5299","file_date_updated":"2020-07-14T12:45:17Z","year":"2015","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"9715","relation":"research_data","status":"public"},{"id":"9772","relation":"research_data","status":"public"}]},"author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova"},{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"volume":10,"date_created":"2018-12-11T11:54:07Z","date_updated":"2023-02-23T14:07:48Z"},{"day":"18","month":"05","article_processing_charge":"No","date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s003","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","short":"B. Trubenova, S. Novak, R. Hager, (2015)."},"type":"research_data_reference","date_created":"2021-08-05T12:55:20Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version","author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"title":"Description of the agent based simulations","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","_id":"9772","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"type":"research_data_reference","related_material":{"record":[{"id":"1827","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","first_name":"Avraham E.","full_name":"Mayo, Avraham E."},{"full_name":"Tlusty, Tsvi","first_name":"Tsvi","last_name":"Tlusty"},{"last_name":"Alon","first_name":"Uri","full_name":"Alon, Uri"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:16:13Z","date_created":"2021-08-05T12:58:07Z","_id":"9773","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","title":"Evolutionary simulation code","status":"public","article_processing_charge":"No","month":"03","day":"23","date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s002","citation":{"ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002."}},{"author":[{"last_name":"Zeljkovic","first_name":"Ilija","full_name":"Zeljkovic, Ilija"},{"full_name":"Okada, Yoshinori","last_name":"Okada","first_name":"Yoshinori"},{"full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"first_name":"Raman","last_name":"Sankar","full_name":"Sankar, Raman"},{"first_name":"Daniel","last_name":"Walkup","full_name":"Walkup, Daniel"},{"full_name":"Zhou, Wenwen","first_name":"Wenwen","last_name":"Zhou"},{"first_name":"Junwei","last_name":"Liu","full_name":"Liu, Junwei"},{"last_name":"Chang","first_name":"Guoqing","full_name":"Chang, Guoqing"},{"full_name":"Wang, Yungjui","first_name":"Yungjui","last_name":"Wang"},{"full_name":"Hasan, Md Z","last_name":"Hasan","first_name":"Md"},{"full_name":"Chou, Fangcheng","last_name":"Chou","first_name":"Fangcheng"},{"full_name":"Lin, Hsin","first_name":"Hsin","last_name":"Lin"},{"full_name":"Bansil, Arun","last_name":"Bansil","first_name":"Arun"},{"full_name":"Fu, Liang","last_name":"Fu","first_name":"Liang"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"volume":14,"date_updated":"2021-01-12T08:22:24Z","date_created":"2018-12-11T11:49:31Z","_id":"981","acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","year":"2015","publisher":"Nature Publishing Group","intvolume":" 14","publication_status":"published","status":"public","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","publist_id":"6419","issue":"3","abstract":[{"text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.","lang":"eng"}],"extern":1,"type":"journal_article","doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","citation":{"chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.","ieee":"I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.4906"}],"oa":1,"publication":"Nature Materials","page":"318 - 324","quality_controlled":0,"day":"01","month":"03"},{"type":"journal_article","publist_id":"6418","issue":"4","abstract":[{"text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.","lang":"eng"}],"extern":1,"_id":"982","year":"2015","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. 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. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","publisher":"American Physical Society","intvolume":" 5","status":"public","publication_status":"published","title":"Criterion for many-body localization-delocalization phase transition","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"volume":5,"date_updated":"2021-01-12T08:22:25Z","date_created":"2018-12-11T11:49:32Z","day":"01","month":"01","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"citation":{"ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015.","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015)."},"publication":"Physical Review X","quality_controlled":0,"date_published":"2015-01-01T00:00:00Z","doi":"10.1103/PhysRevX.5.041047"},{"month":"09","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1501.05155","open_access":"1"}],"external_id":{"arxiv":["1501.05155"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/nphys3461","extern":"1","publist_id":"7955","publication_status":"published","publisher":"Nature Publishing Group","acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation.","year":"2015","date_updated":"2021-01-12T08:22:28Z","date_created":"2018-12-11T11:44:37Z","volume":11,"author":[{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"last_name":"Albrecht","first_name":"S M","full_name":"Albrecht, S M"},{"first_name":"Gediminas","last_name":"Kiršanskas","full_name":"Kiršanskas, Gediminas"},{"full_name":"Chang, W","first_name":"W","last_name":"Chang"},{"last_name":"Kuemmeth","first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand"},{"first_name":"Peter","last_name":"Krogstrup","full_name":"Krogstrup, Peter"},{"last_name":"Jespersen","first_name":"Thomas","full_name":"Jespersen, Thomas"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"full_name":"Flensberg, Karsten","first_name":"Karsten","last_name":"Flensberg"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"day":"14","page":"1017 - 1021","publication":"Nature Physics","citation":{"ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461","ieee":"A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461","chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.","mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021."},"date_published":"2015-09-14T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms."}],"issue":"12","title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","status":"public","intvolume":" 11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"99","oa_version":"Preprint"},{"day":"21","month":"12","article_processing_charge":"No","publication_identifier":{"issn":["0002-9939","1088-6826"]},"publication":"Proceedings of the American Mathematical Society","citation":{"chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","apa":"Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796"},"article_type":"letter_note","quality_controlled":"1","page":"1553-1560","date_published":"2015-12-21T00:00:00Z","doi":"10.1090/proc/12796","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting."}],"issue":"4","extern":"1","year":"2015","_id":"8495","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A note on micro-instability for Hamiltonian systems close to integrable","status":"public","publication_status":"published","publisher":"American Mathematical Society","intvolume":" 144","author":[{"last_name":"Bounemoura","first_name":"Abed","full_name":"Bounemoura, Abed"},{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"}],"date_created":"2020-09-18T10:46:14Z","date_updated":"2021-01-12T08:19:40Z","oa_version":"None","volume":144},{"type":"journal_article","extern":1,"issue":"30","publist_id":"6783","abstract":[{"text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.","lang":"eng"}],"intvolume":" 112","publisher":"National Academy of Sciences","status":"public","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","publication_status":"published","year":"2015","_id":"866","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","volume":112,"date_updated":"2021-01-12T08:20:26Z","date_created":"2018-12-11T11:48:55Z","author":[{"last_name":"Kretz","first_name":"Colin","full_name":"Kretz, Colin A"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"first_name":"Onuralp","last_name":"Soylemez","full_name":"Soylemez, Onuralp"},{"full_name":"Yee, Andrew","last_name":"Yee","first_name":"Andrew"},{"full_name":"Desch, Karl C","last_name":"Desch","first_name":"Karl"},{"first_name":"David","last_name":"Siemieniak","full_name":"Siemieniak, David R"},{"full_name":"Tomberg, Kärt","first_name":"Kärt","last_name":"Tomberg"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Meng","first_name":"Fan","full_name":"Meng, Fan"},{"full_name":"Ginsburg, David B","last_name":"Ginsburg","first_name":"David"}],"day":"28","month":"07","page":"9328 - 9333","quality_controlled":0,"citation":{"chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112","ieee":"C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112"},"publication":"PNAS","doi":"10.1073/pnas.1511328112","date_published":"2015-07-28T00:00:00Z"},{"day":"01","month":"01","doi":"10.1016/j.tig.2014.09.009","date_published":"2015-01-01T00:00:00Z","quality_controlled":0,"page":"24 - 33","publication":"Trends in Genetics","citation":{"mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","apa":"Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009"},"extern":1,"abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}],"publist_id":"6764","issue":"1","type":"journal_article","date_created":"2018-12-11T11:49:01Z","date_updated":"2021-01-12T08:21:16Z","volume":31,"author":[{"first_name":"Dmitry","last_name":"Kondrashov","full_name":"Kondrashov, Dmitry A"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"title":"Topological features of rugged fitness landscapes in sequence space","status":"public","publication_status":"published","intvolume":" 31","publisher":"Elsevier","_id":"886","year":"2015","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) 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 BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME."},{"extern":"1","publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2015","volume":43,"date_created":"2021-01-19T11:01:01Z","date_updated":"2023-02-23T13:46:50Z","author":[{"last_name":"Richet","first_name":"Nicolas","full_name":"Richet, Nicolas"},{"first_name":"Danni","last_name":"Liu","full_name":"Liu, Danni"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"last_name":"Velours","first_name":"Christophe","full_name":"Velours, Christophe"},{"full_name":"Corpet, Armelle","first_name":"Armelle","last_name":"Corpet"},{"first_name":"Albane","last_name":"Gaubert","full_name":"Gaubert, Albane"},{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail","first_name":"May M","full_name":"Bakail, May M"},{"first_name":"Gwenaelle","last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle"},{"first_name":"Raphael","last_name":"Guerois","full_name":"Guerois, Raphael"},{"last_name":"Compper","first_name":"Christel","full_name":"Compper, Christel"},{"first_name":"Arthur","last_name":"Besle","full_name":"Besle, Arthur"},{"full_name":"Guichard, Berengère","last_name":"Guichard","first_name":"Berengère"},{"first_name":"Genevieve","last_name":"Almouzni","full_name":"Almouzni, Genevieve"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"publication_identifier":{"issn":["1362-4962","0305-1048"]},"month":"02","quality_controlled":"1","external_id":{"pmid":["25618846"]},"language":[{"iso":"eng"}],"doi":"10.1093/nar/gkv021","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."}],"intvolume":" 43","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","status":"public","_id":"9017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"No","day":"18","page":"1905-1917","article_type":"original","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.","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.","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.","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.","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.","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","date_published":"2015-02-18T00:00:00Z"}]