[{"title":"Structure-based design of light-controlled proteins","volume":55,"abstract":[{"text":"Small photochromic molecules are widespread in nature and serve as switches for a plethora of light-controlled processes. In a typical photoreceptor, the different geometries and polarities of the photochrome isomers are tightly coupled to functionally relevant conformational changes in the proteins. The past decade has seen extensive efforts to mimic nature and create proteins controlled by synthetic photochromes in the laboratory. Here, we discuss the role of molecular modeling to gain a structural understanding of photochromes and to design light-controlled peptides and proteins. We address several fundamental questions: What are the molecular structures of photochromes, particularly for metastable isomers that cannot be addressed experimentally? How are the structures of bistable photoisomers coupled to the conformational states of peptides and proteins? Can we design light-controlled proteins rapidly and reliably? After an introduction to the principles of molecular modeling, we answer these questions by examining systems that range from the size of isolated photochromes, to that of peptides and large cell surface receptors, each from its unique computational perspective.","lang":"eng"}],"day":"16","date_created":"2018-12-11T12:04:49Z","month":"03","date_published":"2011-03-16T00:00:00Z","publication_status":"published","extern":1,"date_updated":"2021-01-12T07:51:45Z","publisher":"Springer","quality_controlled":0,"status":"public","author":[{"orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Harald Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Isacoff","first_name":"Ehud","full_name":"Isacoff, Ehud Y"}],"year":"2011","page":"233 - 266","doi":"10.1007/978-1-61779-031-7_13","_id":"3724","publist_id":"2504","publication":"Photosensitive Molecules for the Control of Biological Function","type":"book_chapter","citation":{"ieee":"H. L. Janovjak and E. Isacoff, “Structure-based design of light-controlled proteins,” in Photosensitive Molecules for the Control of Biological Function, vol. 55, Springer, 2011, pp. 233–266.","mla":"Janovjak, Harald L., and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” Photosensitive Molecules for the Control of Biological Function, vol. 55, Springer, 2011, pp. 233–66, doi:10.1007/978-1-61779-031-7_13.","apa":"Janovjak, H. L., & Isacoff, E. (2011). Structure-based design of light-controlled proteins. In Photosensitive Molecules for the Control of Biological Function (Vol. 55, pp. 233–266). Springer. https://doi.org/10.1007/978-1-61779-031-7_13","ama":"Janovjak HL, Isacoff E. Structure-based design of light-controlled proteins. In: Photosensitive Molecules for the Control of Biological Function. Vol 55. Springer; 2011:233-266. doi:10.1007/978-1-61779-031-7_13","ista":"Janovjak HL, Isacoff E. 2011.Structure-based design of light-controlled proteins. In: Photosensitive Molecules for the Control of Biological Function. vol. 55, 233–266.","chicago":"Janovjak, Harald L, and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” In Photosensitive Molecules for the Control of Biological Function, 55:233–66. Springer, 2011. https://doi.org/10.1007/978-1-61779-031-7_13.","short":"H.L. Janovjak, E. Isacoff, in:, Photosensitive Molecules for the Control of Biological Function, Springer, 2011, pp. 233–266."},"intvolume":" 55"},{"publist_id":"2457","publication":"Biological Journal of the Linnean Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"None","citation":{"ista":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. 2011. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 102(4), 812–827.","chicago":"Hollatz, Claudia, Sibelle Vilaça, Rodrigo A Fernandes Redondo, Míriam Marmontel, Cyndi Baker, and Fabrício Santos. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological Journal of the Linnean Society. Wiley, 2011. https://doi.org/10.1111/j.1095-8312.2011.01616.x.","short":"C. Hollatz, S. Vilaça, R.A. Fernandes Redondo, M. Marmontel, C. Baker, F. Santos, Biological Journal of the Linnean Society 102 (2011) 812–827.","ieee":"C. Hollatz, S. Vilaça, R. A. Fernandes Redondo, M. Marmontel, C. Baker, and F. Santos, “The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis),” Biological Journal of the Linnean Society, vol. 102, no. 4. Wiley, pp. 812–827, 2011.","mla":"Hollatz, Claudia, et al. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological Journal of the Linnean Society, vol. 102, no. 4, Wiley, 2011, pp. 812–27, doi:10.1111/j.1095-8312.2011.01616.x.","apa":"Hollatz, C., Vilaça, S., Fernandes Redondo, R. A., Marmontel, M., Baker, C., & Santos, F. (2011). The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. Wiley. https://doi.org/10.1111/j.1095-8312.2011.01616.x","ama":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 2011;102(4):812-827. doi:10.1111/j.1095-8312.2011.01616.x"},"intvolume":" 102","status":"public","issue":"4","page":"812 - 827","author":[{"last_name":"Hollatz","full_name":"Hollatz, Claudia","first_name":"Claudia"},{"last_name":"Vilaça","first_name":"Sibelle","full_name":"Vilaça, Sibelle"},{"last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A"},{"last_name":"Marmontel","full_name":"Marmontel, Míriam","first_name":"Míriam"},{"last_name":"Baker","full_name":"Baker, Cyndi","first_name":"Cyndi"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"}],"year":"2011","_id":"3770","doi":"10.1111/j.1095-8312.2011.01616.x","date_updated":"2021-01-12T07:52:05Z","publication_status":"published","extern":"1","month":"04","date_published":"2011-04-01T00:00:00Z","publisher":"Wiley","language":[{"iso":"eng"}],"title":"The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)","volume":102,"date_created":"2018-12-11T12:05:04Z","article_processing_charge":"No","abstract":[{"text":"The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene.","lang":"eng"}],"day":"01"},{"department":[{"_id":"FyKo"}],"article_processing_charge":"No","month":"02","date_published":"2011-02-10T00:00:00Z","publication_status":"published","date_updated":"2025-09-30T08:39:13Z","publisher":"Wiley-Blackwell","year":"2011","issue":"3","status":"public","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","volume":102,"title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","language":[{"iso":"eng"}],"abstract":[{"text":"The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.","lang":"eng"}],"day":"10","date_created":"2018-12-11T12:05:05Z","isi":1,"scopus_import":"1","author":[{"last_name":"Pavan","first_name":"Ana","full_name":"Pavan, Ana"},{"first_name":"Felipe","full_name":"Martins, Felipe","last_name":"Martins"},{"full_name":"Santos, Fabrício","first_name":"Fabrício","last_name":"Santos"},{"last_name":"Ditchfield","full_name":"Ditchfield, Albert","first_name":"Albert"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793"}],"page":"527 - 539","quality_controlled":"1","doi":"10.1111/j.1095-8312.2010.01601.x","_id":"3771","publist_id":"2456","type":"journal_article","publication":"Biological Journal of the Linnean Society","intvolume":" 102","citation":{"short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.","chicago":"Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2010.01601.x.","ista":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 102(3), 527–539.","ama":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 2011;102(3):527-539. doi:10.1111/j.1095-8312.2010.01601.x","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., & Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2010.01601.x","mla":"Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:10.1111/j.1095-8312.2010.01601.x.","ieee":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo, “Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.,” Biological Journal of the Linnean Society, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011."},"external_id":{"isi":["000287193800005"]}},{"external_id":{"pmid":["20502479"],"isi":["000286375300002"]},"citation":{"ieee":"N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","mla":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol. 106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67.","ama":"Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206. doi:10.1038/hdy.2010.67","apa":"Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.","short":"N.H. Barton, Heredity 106 (2011) 205–206.","chicago":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity. Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67."},"intvolume":" 106","publication":"Heredity","type":"journal_article","publist_id":"2449","_id":"3778","doi":"10.1038/hdy.2010.67","page":"205 - 206","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"pmid":1,"scopus_import":"1","isi":1,"date_created":"2018-12-11T12:05:07Z","day":"01","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/"}],"title":"Estimating linkage disequilibria","volume":106,"oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","status":"public","year":"2011","issue":"2","publisher":"Nature Publishing Group","publication_status":"published","date_updated":"2025-09-30T08:38:46Z","date_published":"2011-02-01T00:00:00Z","month":"02","article_processing_charge":"No","department":[{"_id":"NiBa"}],"oa":1},{"type":"journal_article","publist_id":"2446","publication":"Acta Sci. Math. (Szeged)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","acknowledgement":"Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.","citation":{"short":"B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.","chicago":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged). Szegedi Tudományegyetem, 2011.","ista":"Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math. (Szeged). 77(1–2), 359–367.","ama":"Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged). 2011;77(1-2):359-367.","apa":"Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci. Math. (Szeged). Szegedi Tudományegyetem.","mla":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged), vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp. 359–67.","ieee":"B. T. Fasy, “The difference in length of curves in R^n,” Acta Sci. Math. (Szeged), vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011."},"intvolume":" 77","quality_controlled":"1","author":[{"id":"F65D502E-E68D-11E9-9252-C644099818F6","full_name":"Fasy, Brittany Terese","first_name":"Brittany Terese","last_name":"Fasy"}],"status":"public","page":"359 - 367","issue":"1-2","year":"2011","_id":"3781","publication_status":"published","date_updated":"2021-01-12T07:52:09Z","date_published":"2011-01-01T00:00:00Z","month":"01","publisher":"Szegedi Tudományegyetem","language":[{"iso":"eng"}],"title":"The difference in length of curves in R^n","volume":77,"date_created":"2018-12-11T12:05:08Z","day":"01","abstract":[{"text":"We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian.","lang":"eng"}],"department":[{"_id":"HeEd"}]},{"oa":1,"department":[{"_id":"NiBa"}],"article_processing_charge":"No","publication_status":"published","date_updated":"2026-06-18T18:46:40Z","month":"03","article_type":"original","date_published":"2011-03-01T00:00:00Z","publisher":"Cambridge University Press","issue":"2","status":"public","year":"2011","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","volume":91,"main_file_link":[{"url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","date_created":"2018-12-11T12:05:09Z","abstract":[{"lang":"eng","text":"Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus."}],"day":"01","isi":1,"scopus_import":"1","page":"485 - 492","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero","orcid":"0000-0002-0343-8329"},{"last_name":"Guerao","first_name":"Guillermo","full_name":"Guerao, Guillermo"},{"first_name":"Paul","full_name":"Clark, Paul","last_name":"Clark"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"}],"quality_controlled":"1","_id":"3784","doi":"10.1017/S0025315410000287","type":"journal_article","publist_id":"2443","publication":"Journal of the Marine Biological Association of the United Kingdom","intvolume":" 91","external_id":{"isi":["000287940400022"]},"ddc":["570"],"citation":{"apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287","ama":"Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 2011;91(2):485-492. doi:10.1017/S0025315410000287","mla":"Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.","ista":"Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492."}},{"scopus_import":"1","isi":1,"date_created":"2018-12-11T12:05:11Z","abstract":[{"lang":"eng","text":"During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes."}],"day":"01","language":[{"iso":"eng"}],"title":"Cell sorting in development","volume":95,"external_id":{"isi":["000290454200007"]},"citation":{"short":"G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Forces and Tension in Development, Elsevier, 2011, pp. 189–213.","chicago":"Krens, Gabriel, and Carl-Philipp J Heisenberg. “Cell Sorting in Development.” In Forces and Tension in Development, edited by Michel Labouesse, 95:189–213. Elsevier, 2011. https://doi.org/10.1016/B978-0-12-385065-2.00006-2.","ista":"Krens G, Heisenberg C-PJ. 2011.Cell sorting in development. In: Forces and Tension in Development. Current Topics in Developmental Biology, vol. 95, 189–213.","ama":"Krens G, Heisenberg C-PJ. Cell sorting in development. In: Labouesse M, ed. Forces and Tension in Development. Vol 95. Elsevier; 2011:189-213. doi:10.1016/B978-0-12-385065-2.00006-2","apa":"Krens, G., & Heisenberg, C.-P. J. (2011). Cell sorting in development. In M. Labouesse (Ed.), Forces and Tension in Development (Vol. 95, pp. 189–213). Elsevier. https://doi.org/10.1016/B978-0-12-385065-2.00006-2","ieee":"G. Krens and C.-P. J. Heisenberg, “Cell sorting in development,” in Forces and Tension in Development, vol. 95, M. Labouesse, Ed. Elsevier, 2011, pp. 189–213.","mla":"Krens, Gabriel, and Carl-Philipp J. Heisenberg. “Cell Sorting in Development.” Forces and Tension in Development, edited by Michel Labouesse, vol. 95, Elsevier, 2011, pp. 189–213, doi:10.1016/B978-0-12-385065-2.00006-2."},"intvolume":" 95","publication":"Forces and Tension in Development","publist_id":"2436","type":"book_chapter","_id":"3791","doi":"10.1016/B978-0-12-385065-2.00006-2","quality_controlled":"1","page":"189 - 213","author":[{"first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","date_updated":"2025-09-30T08:37:44Z","publication_status":"published","date_published":"2011-01-01T00:00:00Z","month":"01","article_processing_charge":"No","department":[{"_id":"CaHe"}],"oa_version":"None","alternative_title":["Current Topics in Developmental Biology"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","editor":[{"last_name":"Labouesse","full_name":"Labouesse, Michel","first_name":"Michel"}],"corr_author":"1","status":"public","year":"2011"},{"page":"20 - 35","author":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","doi":"10.1007/978-3-642-19391-0_2","_id":"3796","publication":"Rainbow of Computer Science","type":"book_chapter","publist_id":"2427","intvolume":" 6570","citation":{"apa":"Edelsbrunner, H., & Kerber, M. (2011). Covering and packing with spheres by diagonal distortion in R^n. In C. Calude, G. Rozenberg, & A. Salomaa (Eds.), Rainbow of Computer Science (Vol. 6570, pp. 20–35). Springer. https://doi.org/10.1007/978-3-642-19391-0_2","ama":"Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. Rainbow of Computer Science. Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer; 2011:20-35. doi:10.1007/978-3-642-19391-0_2","ieee":"H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal distortion in R^n,” in Rainbow of Computer Science, vol. 6570, C. Calude, G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” Rainbow of Computer Science, edited by Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:10.1007/978-3-642-19391-0_2.","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” In Rainbow of Computer Science, edited by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. https://doi.org/10.1007/978-3-642-19391-0_2.","short":"H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.), Rainbow of Computer Science, Springer, 2011, pp. 20–35.","ista":"Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35."},"ddc":["000"],"file_date_updated":"2020-07-14T12:46:16Z","volume":6570,"series_title":"Dedicated to Hermann Maurer on the Occasion of His 70th Birthday","title":"Covering and packing with spheres by diagonal distortion in R^n","language":[{"iso":"eng"}],"abstract":[{"text":"We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3.","lang":"eng"}],"day":"03","date_created":"2018-12-11T12:05:13Z","scopus_import":"1","pubrep_id":"539","status":"public","year":"2011","has_accepted_license":"1","corr_author":"1","editor":[{"last_name":"Calude","first_name":"Cristian","full_name":"Calude, Cristian"},{"first_name":"Grzegorz","full_name":"Rozenberg, Grzegorz","last_name":"Rozenberg"},{"full_name":"Salomaa, Arto","first_name":"Arto","last_name":"Salomaa"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:16Z","creator":"system","content_type":"application/pdf","checksum":"aaf22b4d7bd4277ffe8db532119cf474","access_level":"open_access","file_size":436875,"file_id":"4640","file_name":"IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf","date_created":"2018-12-12T10:07:42Z","relation":"main_file"}],"alternative_title":["LNCS"],"oa_version":"Submitted Version","oa":1,"department":[{"_id":"HeEd"}],"month":"05","date_published":"2011-05-03T00:00:00Z","date_updated":"2024-10-21T06:03:02Z","publication_status":"published","publisher":"Springer"},{"publisher":"American Physical Society","publication_status":"published","date_updated":"2021-01-12T07:52:44Z","date_published":"2011-07-21T00:00:00Z","article_type":"original","month":"07","article_processing_charge":"No","oa":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","status":"public","year":"2011","extern":"1","date_created":"2018-12-11T11:46:10Z","day":"21","abstract":[{"lang":"eng","text":"We present a detailed study of the local density of states (LDOS) associated with the surface-state band near a step edge of the strong topological insulator Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step edge and is bound to it at some characteristic distance. This bound state is clearly observed in the bulk gap region, while it becomes entangled with the oscillations of the warped surface band at high energy, and with the valence-band states near the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev, 2011] that properly incorporate the three-dimensional nature of the problem to the surface state. Fitting the data at different energies, we can recalculate the LDOS originating from the Dirac band without the contribution of the bulk bands or incoherent tunneling effects. "}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1003.2233","open_access":"1"}],"title":"STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3","volume":84,"external_id":{"arxiv":["1003.2233"]},"citation":{"ieee":"Z. Alpichshev, J. G. Analytis, J. H. Chu, I. R. Fisher, and A. Kapitulnik, “STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4. American Physical Society, 2011.","mla":"Alpichshev, Zhanybek, et al. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4, American Physical Society, 2011, doi:10.1103/PhysRevB.84.041104.","apa":"Alpichshev, Z., Analytis, J. G., Chu, J. H., Fisher, I. R., & Kapitulnik, A. (2011). STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.041104","ama":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 2011;84(4). doi:10.1103/PhysRevB.84.041104","ista":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. 2011. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 84(4).","chicago":"Alpichshev, Zhanybek, J G Analytis, J H Chu, I R Fisher, and A Kapitulnik. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.041104.","short":"Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011)."},"intvolume":" 84","arxiv":1,"publist_id":"7443","type":"journal_article","publication":"Physical Review B - Condensed Matter and Materials Physics","_id":"386","doi":"10.1103/PhysRevB.84.041104","quality_controlled":"1","author":[{"last_name":"Alpichshev","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"},{"last_name":"Analytis","first_name":"J G","full_name":"Analytis, J G"},{"full_name":"Chu, J H","first_name":"J H","last_name":"Chu"},{"full_name":"Fisher, I R","first_name":"I R","last_name":"Fisher"},{"last_name":"Kapitulnik","full_name":"Kapitulnik, A","first_name":"A"}]},{"volume":16,"title":"Computing elevation maxima by searching the Gauss sphere","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"abstract":[{"text":"The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.","lang":"eng"}],"day":"01","date_created":"2018-12-11T12:06:09Z","date_published":"2011-05-01T00:00:00Z","month":"05","publication_status":"published","date_updated":"2021-01-12T07:53:31Z","scopus_import":1,"publisher":"ACM","issue":"2.2","year":"2011","page":"1 - 13","author":[{"first_name":"Bei","full_name":"Wang, Bei","last_name":"Wang"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Morozov","first_name":"Dmitriy","full_name":"Morozov, Dmitriy"}],"status":"public","quality_controlled":"1","doi":"10.1145/1963190.1970375","_id":"3965","type":"journal_article","publist_id":"2161","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Experimental Algorithmics","intvolume":" 16","citation":{"chicago":"Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics. ACM, 2011. https://doi.org/10.1145/1963190.1970375.","short":"B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13.","ista":"Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13.","apa":"Wang, B., Edelsbrunner, H., & Morozov, D. (2011). Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. ACM. https://doi.org/10.1145/1963190.1970375","ama":"Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 2011;16(2.2):1-13. doi:10.1145/1963190.1970375","mla":"Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics, vol. 16, no. 2.2, ACM, 2011, pp. 1–13, doi:10.1145/1963190.1970375.","ieee":"B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching the Gauss sphere,” Journal of Experimental Algorithmics, vol. 16, no. 2.2. ACM, pp. 1–13, 2011."},"oa_version":"None"},{"intvolume":" 2","citation":{"ieee":"L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, and M. Babu, “Epithelial organisation revealed by a network of cellular contacts,” Nature Communications, vol. 2, no. 1. Nature Publishing Group, 2011.","mla":"Escudero, Luis, et al. “Epithelial Organisation Revealed by a Network of Cellular Contacts.” Nature Communications, vol. 2, no. 1, Nature Publishing Group, 2011, doi:10.1038/ncomms1536.","ama":"Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. Epithelial organisation revealed by a network of cellular contacts. Nature Communications. 2011;2(1). doi:10.1038/ncomms1536","apa":"Escudero, L., Costa, L., Kicheva, A., Briscoe, J., Freeman, M., & Babu, M. (2011). Epithelial organisation revealed by a network of cellular contacts. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1536","ista":"Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. 2011. Epithelial organisation revealed by a network of cellular contacts. Nature Communications. 2(1).","short":"L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, M. Babu, Nature Communications 2 (2011).","chicago":"Escudero, Luis, Luciano Costa, Anna Kicheva, James Briscoe, Matthew Freeman, and Madan Babu. “Epithelial Organisation Revealed by a Network of Cellular Contacts.” Nature Communications. Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1536."},"acknowledgement":"We acknowledge the MRC for funding, M.M.B. acknowledges Darwin College, EMBO YIP and Schlumberger Ltd for support. L.M.E. is funded by the Marie Curie and the EMBO fellowships. L.d.F.C. is grateful to FAPESP (05/00587-5) and CNPq (301303/06-1) for financial support. Part of this work was performed during a Visiting Scholarship to L.d.F.C. from St Catharine's College, University of Cambridge. J.B. is supported by the MRC (UK) and A.K. by a FEBS fellowship","publist_id":"5405","publication":"Nature Communications","type":"journal_article","doi":"10.1038/ncomms1536","_id":"1723","author":[{"full_name":"Escudero, Luis M","first_name":"Luis","last_name":"Escudero"},{"first_name":"Luciano","full_name":"Costa, Luciano","last_name":"Costa"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Anna Kicheva"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"last_name":"Freeman","first_name":"Matthew","full_name":"Freeman, Matthew"},{"last_name":"Babu","full_name":"Babu, Madan M","first_name":"Madan"}],"year":"2011","status":"public","issue":"1","quality_controlled":0,"publisher":"Nature Publishing Group","month":"01","date_published":"2011-01-01T00:00:00Z","extern":1,"date_updated":"2021-01-12T06:52:46Z","publication_status":"published","day":"01","abstract":[{"lang":"eng","text":"The emergence of differences in the arrangement of cells is the first step towards the establishment of many organs. Understanding this process is limited by the lack of systematic characterization of epithelial organisation. Here we apply network theory at the scale of individual cells to uncover patterns in cell-to-cell contacts that govern epithelial organisation. We provide an objective characterisation of epithelia using network representation, where cells are nodes and cell contacts are links. The features of individual cells, together with attributes of the cellular network, produce a defining signature that distinguishes epithelia from different organs, species, developmental stages and genetic conditions. The approach permits characterization, quantification and classification of normal and perturbed epithelia, and establishes a framework for understanding molecular mechanisms that underpin the architecture of complex tissues."}],"date_created":"2018-12-11T11:53:40Z","volume":2,"title":"Epithelial organisation revealed by a network of cellular contacts"},{"quality_controlled":0,"author":[{"full_name":"Wartlick, Ortrud","first_name":"Ortrud","last_name":"Wartlick"},{"last_name":"Mumcu","full_name":"Mumcu, Peer","first_name":"Peer"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","first_name":"Anna"},{"first_name":"Thomas","full_name":"Bittig, Thomas","last_name":"Bittig"},{"last_name":"Seum","full_name":"Seum, Carole","first_name":"Carole"},{"last_name":"Jülicher","full_name":"Jülicher, Frank","first_name":"Frank"},{"full_name":"González-Gaitán, Marcos A","first_name":"Marcos","last_name":"González Gaitán"}],"year":"2011","page":"1154 - 1159","status":"public","issue":"6021","_id":"1724","doi":"10.1126/science.1200037","publication":"Science","type":"journal_article","publist_id":"5406","citation":{"apa":"Wartlick, O., Mumcu, P., Kicheva, A., Bittig, T., Seum, C., Jülicher, F., & González Gaitán, M. (2011). Dynamics of Dpp signaling and proliferation control. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1200037","ama":"Wartlick O, Mumcu P, Kicheva A, et al. Dynamics of Dpp signaling and proliferation control. Science. 2011;331(6021):1154-1159. doi:10.1126/science.1200037","mla":"Wartlick, Ortrud, et al. “Dynamics of Dpp Signaling and Proliferation Control.” Science, vol. 331, no. 6021, American Association for the Advancement of Science, 2011, pp. 1154–59, doi:10.1126/science.1200037.","ieee":"O. Wartlick et al., “Dynamics of Dpp signaling and proliferation control,” Science, vol. 331, no. 6021. American Association for the Advancement of Science, pp. 1154–1159, 2011.","chicago":"Wartlick, Ortrud, Peer Mumcu, Anna Kicheva, Thomas Bittig, Carole Seum, Frank Jülicher, and Marcos González Gaitán. “Dynamics of Dpp Signaling and Proliferation Control.” Science. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1200037.","short":"O. Wartlick, P. Mumcu, A. Kicheva, T. Bittig, C. Seum, F. Jülicher, M. González Gaitán, Science 331 (2011) 1154–1159.","ista":"Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González Gaitán M. 2011. Dynamics of Dpp signaling and proliferation control. Science. 331(6021), 1154–1159."},"acknowledgement":"P.M., T.B., and F.J. were supported by the Max-Planck-Gesellschaft. O.W., A.K., C.S., and M.G.-G. were supported by Geneva University and by European Research Council advanced investigator grant (SARA), SystemsX (LipidX), Swiss National Science Foundation (SNF), National Centre of Competence in Research (NCCR) chemical biology and Frontiers in Genetics and R'equip grants","intvolume":" 331","title":"Dynamics of Dpp signaling and proliferation control","volume":331,"date_created":"2018-12-11T11:53:40Z","day":"04","abstract":[{"lang":"eng","text":"Morphogens, such as Decapentaplegic (Dpp) in the fly imaginal discs, form graded concentration profiles that control patterning and growth of developing organs. In the imaginal discs, proliferative growth is homogeneous in space, posing the conundrum of how morphogen concentration gradients could control position-independent growth. To understand the mechanism of proliferation control by the Dpp gradient, we quantified Dpp concentration and signaling levels during wing disc growth. Both Dpp concentration and signaling gradients scale with tissue size during development. On average, cells divide when Dpp signaling levels have increased by 50%. Our observations are consistent with a growth control mechanism based on temporal changes of cellular morphogen signaling levels. For a scaling gradient, this mechanism generates position-independent growth rates."}],"date_updated":"2021-01-12T06:52:46Z","publication_status":"published","extern":1,"month":"03","date_published":"2011-03-04T00:00:00Z","publisher":"American Association for the Advancement of Science"},{"type":"journal_article","publist_id":"5370","publication":"ACS Nano","external_id":{"arxiv":["1110.5668"]},"acknowledgement":"This work was supported by the Agence Nationale de la Recherche (ANR) through the ACCESS and COHESION projects and by the European Commission through the Chemtronics program MEST-CT-2005-020513","citation":{"mla":"Mongillo, Massimo, et al. “Joule-Assisted Silicidation for Short-Channel Silicon Nanowire Devices.” ACS Nano, vol. 5, no. 9, American Chemical Society, 2011, pp. 7117–23, doi:10.1021/nn202524j.","ieee":"M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, and S. De Franceschi, “Joule-assisted silicidation for short-channel silicon nanowire devices,” ACS Nano, vol. 5, no. 9. American Chemical Society, pp. 7117–7123, 2011.","apa":"Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., Sanquer, M., & De Franceschi, S. (2011). Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn202524j","ama":"Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. 2011;5(9):7117-7123. doi:10.1021/nn202524j","ista":"Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. 2011. Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. 5(9), 7117–7123.","chicago":"Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile, Marc Sanquer, and Silvano De Franceschi. “Joule-Assisted Silicidation for Short-Channel Silicon Nanowire Devices.” ACS Nano. American Chemical Society, 2011. https://doi.org/10.1021/nn202524j.","short":"M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, S. De Franceschi, ACS Nano 5 (2011) 7117–7123."},"intvolume":" 5","arxiv":1,"quality_controlled":"1","page":"7117 - 7123","author":[{"last_name":"Mongillo","full_name":"Mongillo, Massimo","first_name":"Massimo"},{"full_name":"Spathis, Panayotis","first_name":"Panayotis","last_name":"Spathis"},{"last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gentile","first_name":"Pascal","full_name":"Gentile, Pascal"},{"first_name":"Marc","full_name":"Sanquer, Marc","last_name":"Sanquer"},{"last_name":"De Franceschi","full_name":"De Franceschi, Silvano","first_name":"Silvano"}],"_id":"1754","doi":"10.1021/nn202524j","extern":"1","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1110.5668","open_access":"1"}],"title":"Joule-assisted silicidation for short-channel silicon nanowire devices","volume":5,"date_created":"2018-12-11T11:53:50Z","abstract":[{"text":"We report on a technique enabling electrical control of the contact silicidation process in silicon nanowire devices. Undoped silicon nanowires were contacted by pairs of nickel electrodes and each contact was selectively silicided by means of the Joule effect. By a realtime monitoring of the nanowire electrical resistance during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel- silicide devices with controlled silicon channel length down to 8 nm. ","lang":"eng"}],"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","issue":"9","status":"public","year":"2011","date_updated":"2021-01-12T06:52:59Z","publication_status":"published","date_published":"2011-09-27T00:00:00Z","month":"09","publisher":"American Chemical Society","oa":1},{"citation":{"chicago":"Katsaros, Georgios, Vitaly Golovach, Panayotis Spathis, Natalia Ares, Mathieu Stoffel, Frank Fournel, Oliver Schmidt, Leonid Glazman, and Silvano De Franceschi. “Observation of Spin-Selective Tunneling in Sige Nanocrystals.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.246601.","short":"G. Katsaros, V. Golovach, P. Spathis, N. Ares, M. Stoffel, F. Fournel, O. Schmidt, L. Glazman, S. De Franceschi, Physical Review Letters 107 (2011).","ista":"Katsaros G, Golovach V, Spathis P, Ares N, Stoffel M, Fournel F, Schmidt O, Glazman L, De Franceschi S. 2011. Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. 107(24).","apa":"Katsaros, G., Golovach, V., Spathis, P., Ares, N., Stoffel, M., Fournel, F., … De Franceschi, S. (2011). Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.246601","ama":"Katsaros G, Golovach V, Spathis P, et al. Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. 2011;107(24). doi:10.1103/PhysRevLett.107.246601","mla":"Katsaros, Georgios, et al. “Observation of Spin-Selective Tunneling in Sige Nanocrystals.” Physical Review Letters, vol. 107, no. 24, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.246601.","ieee":"G. Katsaros et al., “Observation of spin-selective tunneling in sige nanocrystals,” Physical Review Letters, vol. 107, no. 24. American Physical Society, 2011."},"acknowledgement":"The work was supported by the Agence Nationale de la Recherche (through the ACCESS and COHESION projects), U.S. DOE Contract No. DE-FG02-08ER46482 (Yale), and the Nanosciences Foundation at Grenoble, France. G. K. acknowledges support from the Deutsche Forschungsgemeinschaft","intvolume":" 107","type":"journal_article","publist_id":"5369","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.107.246601","_id":"1755","quality_controlled":0,"author":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Georgios Katsaros"},{"last_name":"Golovach","full_name":"Golovach, Vitaly N","first_name":"Vitaly"},{"first_name":"Panayotis","full_name":"Spathis, Panayotis N","last_name":"Spathis"},{"first_name":"Natalia","full_name":"Ares, Natalia","last_name":"Ares"},{"last_name":"Stoffel","first_name":"Mathieu","full_name":"Stoffel, Mathieu"},{"last_name":"Fournel","first_name":"Frank","full_name":"Fournel, Frank"},{"last_name":"Schmidt","full_name":"Schmidt, Oliver G","first_name":"Oliver"},{"last_name":"Glazman","full_name":"Glazman, Leonid I","first_name":"Leonid"},{"full_name":"De Franceschi, Silvano","first_name":"Silvano","last_name":"De Franceschi"}],"status":"public","issue":"24","year":"2011","publisher":"American Physical Society","date_published":"2011-12-07T00:00:00Z","month":"12","extern":1,"publication_status":"published","date_updated":"2021-01-12T06:53:00Z","day":"07","abstract":[{"text":"Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal leads is reported. The spin selectivity arises from an interplay of the orbital effect of the magnetic field with the strong spin-orbit interaction present in the valence band of the semiconductor. We demonstrate both experimentally and theoretically that spin-selective tunneling in semiconductor nanostructures can be achieved without the use of ferromagnetic contacts. The reported effect, which relies on mixing the light and heavy holes, should be observable in a broad class of quantum-dot systems formed in semiconductors with a degenerate valence band.","lang":"eng"}],"date_created":"2018-12-11T11:53:50Z","title":"Observation of spin-selective tunneling in sige nanocrystals","main_file_link":[{"url":"http://arxiv.org/abs/1107.3919","open_access":"1"}],"oa":1,"volume":107},{"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1103.4609","open_access":"1"}],"language":[{"iso":"eng"}],"title":"Imprint of accretion disk-induced migration on gravitational waves from extreme mass ratio inspirals","volume":107,"date_created":"2024-09-06T07:26:09Z","day":"21","abstract":[{"lang":"eng","text":"We study the effects of a thin gaseous accretion disk on the inspiral of a stellar--mass black hole into a supermassive black hole. We construct a phenomenological angular momentum transport equation that reproduces known disk effects. Disk torques modify the gravitational wave phase evolution to detectable levels with LISA for reasonable disk parameters. The Fourier transform of disk-modified waveforms acquires a correction with a different frequency trend than post-Newtonian vacuum terms. Such inspirals could be used to detect accretion disks with LISA and to probe their physical parameters."}],"scopus_import":"1","extern":"1","quality_controlled":"1","author":[{"last_name":"Yunes","full_name":"Yunes, Nicolás","first_name":"Nicolás"},{"first_name":"Bence","full_name":"Kocsis, Bence","last_name":"Kocsis"},{"first_name":"Abraham","full_name":"Loeb, Abraham","last_name":"Loeb"},{"first_name":"Zoltán","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"}],"_id":"17647","doi":"10.1103/physrevlett.107.171103","publication":"Physical Review Letters","type":"journal_article","external_id":{"arxiv":["1103.4609"]},"citation":{"short":"N. Yunes, B. Kocsis, A. Loeb, Z. Haiman, Physical Review Letters 107 (2011).","chicago":"Yunes, Nicolás, Bence Kocsis, Abraham Loeb, and Zoltán Haiman. “Imprint of Accretion Disk-Induced Migration on Gravitational Waves from Extreme Mass Ratio Inspirals.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/physrevlett.107.171103.","ista":"Yunes N, Kocsis B, Loeb A, Haiman Z. 2011. Imprint of accretion disk-induced migration on gravitational waves from extreme mass ratio inspirals. Physical Review Letters. 107(17), 171103.","ama":"Yunes N, Kocsis B, Loeb A, Haiman Z. Imprint of accretion disk-induced migration on gravitational waves from extreme mass ratio inspirals. Physical Review Letters. 2011;107(17). doi:10.1103/physrevlett.107.171103","apa":"Yunes, N., Kocsis, B., Loeb, A., & Haiman, Z. (2011). Imprint of accretion disk-induced migration on gravitational waves from extreme mass ratio inspirals. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.107.171103","ieee":"N. Yunes, B. Kocsis, A. Loeb, and Z. Haiman, “Imprint of accretion disk-induced migration on gravitational waves from extreme mass ratio inspirals,” Physical Review Letters, vol. 107, no. 17. American Physical Society, 2011.","mla":"Yunes, Nicolás, et al. “Imprint of Accretion Disk-Induced Migration on Gravitational Waves from Extreme Mass Ratio Inspirals.” Physical Review Letters, vol. 107, no. 17, 171103, American Physical Society, 2011, doi:10.1103/physrevlett.107.171103."},"intvolume":" 107","arxiv":1,"oa":1,"article_processing_charge":"No","article_number":"171103","date_updated":"2024-09-24T12:44:50Z","publication_status":"published","month":"10","date_published":"2011-10-21T00:00:00Z","article_type":"original","publisher":"American Physical Society","year":"2011","status":"public","issue":"17","publication_identifier":{"issn":["0031-9007","1079-7114"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint"},{"status":"public","issue":"4","year":"2011","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1550-7998","1550-2368"]},"article_number":"043529","article_processing_charge":"No","oa":1,"publisher":"American Physical Society","date_updated":"2024-09-25T07:25:48Z","publication_status":"published","date_published":"2011-08-24T00:00:00Z","article_type":"original","month":"08","_id":"17661","doi":"10.1103/physrevd.84.043529","author":[{"full_name":"Yang, Xiuyuan","first_name":"Xiuyuan","last_name":"Yang"},{"last_name":"Kratochvil","first_name":"Jan M.","full_name":"Kratochvil, Jan M."},{"last_name":"Wang","first_name":"Sheng","full_name":"Wang, Sheng"},{"full_name":"Lim, Eugene A.","first_name":"Eugene A.","last_name":"Lim"},{"full_name":"Haiman, Zoltán","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"},{"last_name":"May","full_name":"May, Morgan","first_name":"Morgan"}],"quality_controlled":"1","intvolume":" 84","arxiv":1,"external_id":{"arxiv":["1109.6333"]},"citation":{"chicago":"Yang, Xiuyuan, Jan M. Kratochvil, Sheng Wang, Eugene A. Lim, Zoltán Haiman, and Morgan May. “Cosmological Information in Weak Lensing Peaks.” Physical Review D. American Physical Society, 2011. https://doi.org/10.1103/physrevd.84.043529.","short":"X. Yang, J.M. Kratochvil, S. Wang, E.A. Lim, Z. Haiman, M. May, Physical Review D 84 (2011).","ista":"Yang X, Kratochvil JM, Wang S, Lim EA, Haiman Z, May M. 2011. Cosmological information in weak lensing peaks. Physical Review D. 84(4), 043529.","apa":"Yang, X., Kratochvil, J. M., Wang, S., Lim, E. A., Haiman, Z., & May, M. (2011). Cosmological information in weak lensing peaks. Physical Review D. American Physical Society. https://doi.org/10.1103/physrevd.84.043529","ama":"Yang X, Kratochvil JM, Wang S, Lim EA, Haiman Z, May M. Cosmological information in weak lensing peaks. Physical Review D. 2011;84(4). doi:10.1103/physrevd.84.043529","mla":"Yang, Xiuyuan, et al. “Cosmological Information in Weak Lensing Peaks.” Physical Review D, vol. 84, no. 4, 043529, American Physical Society, 2011, doi:10.1103/physrevd.84.043529.","ieee":"X. Yang, J. M. Kratochvil, S. Wang, E. A. Lim, Z. Haiman, and M. May, “Cosmological information in weak lensing peaks,” Physical Review D, vol. 84, no. 4. American Physical Society, 2011."},"publication":"Physical Review D","type":"journal_article","date_created":"2024-09-06T07:39:00Z","abstract":[{"lang":"eng","text":"Recent studies have shown that the number counts of convergence peaks N(kappa) in weak lensing (WL) maps, expected from large forthcoming surveys, can be a useful probe of cosmology. We follow up on this finding, and use a suite of WL convergence maps, obtained from ray-tracing N-body simulations, to study (i) the physical origin of WL peaks with different heights, and (ii) whether the peaks contain information beyond the convergence power spectrum P_ell. In agreement with earlier work, we find that high peaks (with amplitudes >~ 3.5 sigma, where sigma is the r.m.s. of the convergence kappa) are typically dominated by a single massive halo. In contrast, medium-height peaks (~0.5-1.5 sigma) cannot be attributed to a single collapsed dark matter halo, and are instead created by the projection of multiple (typically, 4-8) halos along the line of sight, and by random galaxy shape noise. Nevertheless, these peaks dominate the sensitivity to the cosmological parameters w, sigma_8, and Omega_m. We find that the peak height distribution and its dependence on cosmology differ significantly from predictions in a Gaussian random field. We directly compute the marginalized errors on w, sigma_8, and Omega_m from the N(kappa) + P_ell combination, including redshift tomography with source galaxies at z_s=1 and z_s=2. We find that the N(kappa) + P_ell combination has approximately twice the cosmological sensitivity compared to P_ell alone. These results demonstrate that N(kappa) contains non-Gaussian information complementary to the power spectrum."}],"day":"24","volume":84,"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1109.6333"}],"title":"Cosmological information in weak lensing peaks","scopus_import":"1","extern":"1"},{"type":"journal_article","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"chicago":"Wolcott-Green, J., and Zoltán Haiman. “Suppression of HD Cooling in Protogalactic Gas Clouds by Lyman-Werner Radiation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2011. https://doi.org/10.1111/j.1365-2966.2010.18080.x.","short":"J. Wolcott-Green, Z. Haiman, Monthly Notices of the Royal Astronomical Society 412 (2011) 2603–2616.","ista":"Wolcott-Green J, Haiman Z. 2011. Suppression of HD cooling in protogalactic gas clouds by Lyman-Werner radiation. Monthly Notices of the Royal Astronomical Society. 412(4), 2603–2616.","apa":"Wolcott-Green, J., & Haiman, Z. (2011). Suppression of HD cooling in protogalactic gas clouds by Lyman-Werner radiation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1111/j.1365-2966.2010.18080.x","ama":"Wolcott-Green J, Haiman Z. Suppression of HD cooling in protogalactic gas clouds by Lyman-Werner radiation. Monthly Notices of the Royal Astronomical Society. 2011;412(4):2603-2616. doi:10.1111/j.1365-2966.2010.18080.x","ieee":"J. Wolcott-Green and Z. Haiman, “Suppression of HD cooling in protogalactic gas clouds by Lyman-Werner radiation,” Monthly Notices of the Royal Astronomical Society, vol. 412, no. 4. Oxford University Press, pp. 2603–2616, 2011.","mla":"Wolcott-Green, J., and Zoltán Haiman. “Suppression of HD Cooling in Protogalactic Gas Clouds by Lyman-Werner Radiation.” Monthly Notices of the Royal Astronomical Society, vol. 412, no. 4, Oxford University Press, 2011, pp. 2603–16, doi:10.1111/j.1365-2966.2010.18080.x."},"intvolume":" 412","quality_controlled":"1","author":[{"first_name":"J.","full_name":"Wolcott-Green, J.","last_name":"Wolcott-Green"},{"last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","full_name":"Haiman, Zoltán"}],"page":"2603-2616","_id":"17676","doi":"10.1111/j.1365-2966.2010.18080.x","scopus_import":"1","extern":"1","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1111/j.1365-2966.2010.18080.x","open_access":"1"}],"title":"Suppression of HD cooling in protogalactic gas clouds by Lyman-Werner radiation","volume":412,"date_created":"2024-09-06T07:52:22Z","day":"08","abstract":[{"lang":"eng","text":"It has been shown that HD molecules can form efficiently in metal-free gas collapsing into massive protogalactic halos at high redshift. The resulting radiative cooling by HD can lower the gas temperature to that of the cosmic microwave background, T_CMB=2.7(1+z)K, significantly below the temperature of a few 100 K achievable via H_2-cooling alone, and thus reduce the masses of the first generation of stars. Here we consider the suppression of HD-cooling by UV irradiation in the Lyman-Werner (LW) bands. We include photo-dissociation of both H_2 and HD, and explicitly compute the self-shielding and shielding of both molecules by neutral hydrogen as well as the shielding of HD by H_2. We use a simplified dynamical collapse model, and follow the chemical and thermal evolution of the gas, in the presence of a UV background. We find that a LW flux of J_crit = 1e-22 erg/cm^2/sr/s/Hz is able to suppress HD cooling and thus prevent collapsing primordial gas from reaching temperatures below 100 K. The main reason for the lack of HD cooling for J>J_crit is the partial photo-dissociation of H_2, which prevents the gas from reaching sufficiently low temperatures (T<150K) for HD to become the dominant coolant; direct HD photo-dissociation is unimportant except for a narrow range of fluxes and column densities. Since the prevention of HD-cooling requires only partial H_2 photo-dissociation, the critical flux J_crit is modest, and is below the UV background required to reionize the universe at redshift z=10-20. We conclude that HD-cooling can reduce the masses of typical stars only in rare halos forming well before the epoch of reionization."}],"publication_identifier":{"issn":["0035-8711"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","alternative_title":["Suppression of HD cooling in primordial gas"],"status":"public","year":"2011","issue":"4","date_updated":"2024-09-25T08:47:23Z","publication_status":"published","month":"04","date_published":"2011-04-08T00:00:00Z","article_type":"original","publisher":"Oxford University Press","oa":1,"article_processing_charge":"No"},{"extern":"1","scopus_import":"1","abstract":[{"text":"The gravitational waves (GWs) emitted by inspiralling binary black holes, expected to be detected by the Laser Interferometer Space Antenna (LISA), could be used to determine the luminosity distance to these sources with the unprecedented precision of ≲1 per cent. We study cosmological parameter constraints from such standard sirens, in the presence of gravitational lensing by large-scale structure. Lensing introduces magnification with a probability distribution function (PDF) whose shape has significant skewness and kurtosis, and depends on cosmological parameters. We use Monte Carlo simulations to generate mock samples of standard sirens, including a small intrinsic scatter, as well as the additional, larger scatter from lensing, in their inferred distances. We derive constraints on cosmological parameters, by simultaneously fitting the mean and the distribution of the residuals on the distance versus redshift (dL–z) Hubble diagram. We find that for standard sirens at redshift z≈ 1, the sensitivity to a single cosmological parameter, such as the matter density Ωm, or the dark energy equation of state w, is ∼50–80 per cent tighter when the lensing PDF is used, compared to the sensitivity derived from a Gaussian PDF with the same variance. When these two parameters are constrained simultaneously, the non-Gaussian shape yields a further enhanced improvement (by ∼120 per cent), owing to the correlation between the parameters. The sensitivity to the amplitude of the matter power spectrum, σ8 from the cosmological dependence of the PDF alone, however, is ∼20 per cent worse than that from the Gaussian PDF. The improvements for Ωm and w arise purely from the non-Gaussian shape of the lensing PDF and can be attributed specifically to the sharpness of the peak of this PDF (i.e. to a finite kurtosis); the dependence of the PDF on these parameters does not improve constraints relative to those available from the mean dL–z relation. At higher redshifts, the PDF resembles a Gaussian more closely, and the effects of the non-Gaussianities become less prominent. These results highlight the importance of obtaining an accurate and reliable PDF of the lensing convergence, in order to realize the full potential of standard sirens as cosmological probes.","lang":"eng"}],"day":"21","date_created":"2024-09-06T08:07:44Z","title":"Cosmology with standard sirens: The importance of the shape of the lensing magnification distribution","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1111/j.1365-2966.2010.17607.x","open_access":"1"}],"volume":411,"citation":{"chicago":"Shang, Cien, and Zoltán Haiman. “Cosmology with Standard Sirens: The Importance of the Shape of the Lensing Magnification Distribution.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2011. https://doi.org/10.1111/j.1365-2966.2010.17607.x.","short":"C. Shang, Z. Haiman, Monthly Notices of the Royal Astronomical Society 411 (2011) 9–22.","ista":"Shang C, Haiman Z. 2011. Cosmology with standard sirens: The importance of the shape of the lensing magnification distribution. Monthly Notices of the Royal Astronomical Society. 411(1), 9–22.","apa":"Shang, C., & Haiman, Z. (2011). Cosmology with standard sirens: The importance of the shape of the lensing magnification distribution. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1111/j.1365-2966.2010.17607.x","ama":"Shang C, Haiman Z. Cosmology with standard sirens: The importance of the shape of the lensing magnification distribution. Monthly Notices of the Royal Astronomical Society. 2011;411(1):9-22. doi:10.1111/j.1365-2966.2010.17607.x","ieee":"C. Shang and Z. Haiman, “Cosmology with standard sirens: The importance of the shape of the lensing magnification distribution,” Monthly Notices of the Royal Astronomical Society, vol. 411, no. 1. Oxford University Press, pp. 9–22, 2011.","mla":"Shang, Cien, and Zoltán Haiman. “Cosmology with Standard Sirens: The Importance of the Shape of the Lensing Magnification Distribution.” Monthly Notices of the Royal Astronomical Society, vol. 411, no. 1, Oxford University Press, 2011, pp. 9–22, doi:10.1111/j.1365-2966.2010.17607.x."},"intvolume":" 411","publication":"Monthly Notices of the Royal Astronomical Society","type":"journal_article","doi":"10.1111/j.1365-2966.2010.17607.x","_id":"17681","quality_controlled":"1","author":[{"last_name":"Shang","full_name":"Shang, Cien","first_name":"Cien"},{"last_name":"Haiman","first_name":"Zoltán","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"}],"page":"9-22","publisher":"Oxford University Press","article_type":"original","date_published":"2011-01-21T00:00:00Z","month":"01","publication_status":"published","date_updated":"2024-09-25T09:04:38Z","article_processing_charge":"No","oa":1,"alternative_title":["WL and GW standard sirens"],"oa_version":"Published Version","publication_identifier":{"issn":["0035-8711"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","status":"public","year":"2011"},{"month":"11","date_published":"2011-11-16T00:00:00Z","article_type":"original","publication_status":"published","date_updated":"2024-09-25T09:53:37Z","publisher":"Oxford University Press","oa":1,"article_processing_charge":"No","publication_identifier":{"issn":["0035-8711"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["H 2 self-shielding in 3D simulations"],"oa_version":"Published Version","year":"2011","status":"public","issue":"2","scopus_import":"1","extern":"1","title":"Photodissociation of H2 in protogalaxies: Modelling self-shielding in three-dimensional simulations","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1111/j.1365-2966.2011.19538.x","open_access":"1"}],"volume":418,"abstract":[{"lang":"eng","text":"The ability of primordial gas to cool in proto-galactic haloes exposed to Lyman-Werner (LW) radiation is critically dependent on the self-shielding of H_2. We perform radiative transfer calculations of LW line photons, post-processing outputs from three-dimensional adaptive mesh refinement (AMR) simulations of haloes with T_vir > 10^4 K at redshifts around z=10. We calculate the optically thick photodissociation rate numerically, including the effects of density, temperature, and velocity gradients in the gas, as well as line overlap and shielding of H_2 by HI, over a large number of sight-lines. In low-density regions (n<10^4 cm^-3) the dissociation rates exceed those obtained using most previous approximations by more than an order of magnitude; the correction is smaller at higher densities. We trace the origin of the deviations primarily to inaccuracies of (i) the most common fitting formula (Draine & Bertoldi 1996) for the suppression of the dissociation rate and (ii) estimates for the effective shielding column density from local properties of the gas. The combined effects of gas temperature and velocity gradients are comparatively less important, typically altering the spherically averaged rate only by a factor of less than two. We present a simple modification to the DB96 fitting formula for the optically thick rate which improves agreement with our numerical results to within approx. 15 per cent, and can be adopted in future simulations. We find that estimates for the effective shielding column can be improved by using the local Sobolev length. Our correction to the H_2 self-shielding reduces the critical LW flux to suppress H_2-cooling in T_vir>10^4 K haloes by an order of magnitude; this increases the number of such haloes in which supermassive (approx. M=10^5 M_sun) black holes may have formed."}],"day":"16","date_created":"2024-09-06T08:37:08Z","publication":"Monthly Notices of the Royal Astronomical Society","type":"journal_article","citation":{"apa":"Wolcott-Green, J., Haiman, Z., & Bryan, G. L. (2011). Photodissociation of H2 in protogalaxies: Modelling self-shielding in three-dimensional simulations. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1111/j.1365-2966.2011.19538.x","ama":"Wolcott-Green J, Haiman Z, Bryan GL. Photodissociation of H2 in protogalaxies: Modelling self-shielding in three-dimensional simulations. Monthly Notices of the Royal Astronomical Society. 2011;418(2):838-852. doi:10.1111/j.1365-2966.2011.19538.x","ieee":"J. Wolcott-Green, Z. Haiman, and G. L. Bryan, “Photodissociation of H2 in protogalaxies: Modelling self-shielding in three-dimensional simulations,” Monthly Notices of the Royal Astronomical Society, vol. 418, no. 2. Oxford University Press, pp. 838–852, 2011.","mla":"Wolcott-Green, J., et al. “Photodissociation of H2 in Protogalaxies: Modelling Self-Shielding in Three-Dimensional Simulations.” Monthly Notices of the Royal Astronomical Society, vol. 418, no. 2, Oxford University Press, 2011, pp. 838–52, doi:10.1111/j.1365-2966.2011.19538.x.","chicago":"Wolcott-Green, J., Zoltán Haiman, and G. L. Bryan. “Photodissociation of H2 in Protogalaxies: Modelling Self-Shielding in Three-Dimensional Simulations.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2011. https://doi.org/10.1111/j.1365-2966.2011.19538.x.","short":"J. Wolcott-Green, Z. Haiman, G.L. Bryan, Monthly Notices of the Royal Astronomical Society 418 (2011) 838–852.","ista":"Wolcott-Green J, Haiman Z, Bryan GL. 2011. Photodissociation of H2 in protogalaxies: Modelling self-shielding in three-dimensional simulations. Monthly Notices of the Royal Astronomical Society. 418(2), 838–852."},"intvolume":" 418","quality_controlled":"1","page":"838-852","author":[{"full_name":"Wolcott-Green, J.","first_name":"J.","last_name":"Wolcott-Green"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán","last_name":"Haiman"},{"last_name":"Bryan","first_name":"G. L.","full_name":"Bryan, G. L."}],"doi":"10.1111/j.1365-2966.2011.19538.x","_id":"17690"},{"year":"2011","status":"public","issue":"7341","publication_identifier":{"issn":["0028-0836","1476-4687"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","oa":1,"article_processing_charge":"No","month":"04","date_published":"2011-04-06T00:00:00Z","article_type":"original","date_updated":"2024-09-25T11:25:52Z","publication_status":"published","publisher":"Springer Science and Business Media LLC","quality_controlled":"1","author":[{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán","last_name":"Haiman"}],"page":"47-48","doi":"10.1038/472047a","_id":"17701","type":"journal_article","publication":"Nature","citation":{"chicago":"Haiman, Zoltán. “A Smoother End to the Dark Ages.” Nature. Springer Science and Business Media LLC, 2011. https://doi.org/10.1038/472047a.","short":"Z. Haiman, Nature 472 (2011) 47–48.","ista":"Haiman Z. 2011. A smoother end to the dark ages. Nature. 472(7341), 47–48.","apa":"Haiman, Z. (2011). A smoother end to the dark ages. Nature. Springer Science and Business Media LLC. https://doi.org/10.1038/472047a","ama":"Haiman Z. A smoother end to the dark ages. Nature. 2011;472(7341):47-48. doi:10.1038/472047a","mla":"Haiman, Zoltán. “A Smoother End to the Dark Ages.” Nature, vol. 472, no. 7341, Springer Science and Business Media LLC, 2011, pp. 47–48, doi:10.1038/472047a.","ieee":"Z. Haiman, “A smoother end to the dark ages,” Nature, vol. 472, no. 7341. Springer Science and Business Media LLC, pp. 47–48, 2011."},"external_id":{"arxiv":["1104.1189"]},"arxiv":1,"intvolume":" 472","title":"A smoother end to the dark ages","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1104.1189"}],"volume":472,"day":"06","abstract":[{"lang":"eng","text":"Independent lines of evidence suggest that the first stars, which ended the cosmic dark ages, came in pairs, rather than singly. This could change the prevailing view that the early Universe had a Swiss-cheese-like appearance."}],"date_created":"2024-09-06T08:47:22Z","scopus_import":"1","extern":"1"}]