[{"file":[{"checksum":"98bc02e3793072e279ec8d364b381ff3","file_name":"2013_ICALP_Boker.pdf","file_size":276982,"file_id":"7857","date_updated":"2020-07-14T12:44:48Z","date_created":"2020-05-15T11:05:50Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":"      7966","ddc":["000"],"day":"01","month":"07","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:48Z","conference":{"end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","location":"Riga, Latvia"},"article_processing_charge":"No","date_updated":"2020-08-11T10:09:09Z","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-39212-2_11","date_published":"2013-07-01T00:00:00Z","author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi"},{"last_name":"Kuperberg","first_name":"Denis","full_name":"Kuperberg, Denis"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"},{"last_name":"Skrzypczak","first_name":"Michał","full_name":"Skrzypczak, Michał"}],"quality_controlled":"1","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":7966,"page":"89 - 100","has_accepted_license":"1","year":"2013","_id":"1387","issue":"PART 2","status":"public","acknowledgement":"and ERC Grant QUALITY.","oa":1,"citation":{"mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>.","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>."},"publisher":"Springer","department":[{"_id":"ToHe"}],"title":"Nondeterminism in the presence of a diverse or unknown future","publist_id":"5823","date_created":"2018-12-11T11:51:44Z","ec_funded":1,"oa_version":"Submitted Version","series_title":"Lecture Notes in Computer Science","abstract":[{"lang":"eng","text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata."}]},{"month":"09","language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"day":"05","main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2021-02-22T11:28:36Z","file_id":"9176","date_updated":"2021-02-22T11:28:36Z","file_size":1514906,"file_name":"2013_Zufferey_thesis_final.pdf","checksum":"ed2d7b52933d134e8dc69d569baa284e"},{"date_created":"2021-11-16T14:42:52Z","content_type":"application/pdf","creator":"cchlebak","access_level":"closed","relation":"main_file","file_name":"2013_Zufferey_thesis_final_pdfa.pdf","checksum":"cecc4c4b14225bee973d32e3dba91a55","file_size":1378313,"date_updated":"2021-11-17T13:47:58Z","file_id":"10298"}],"publication_status":"published","degree_awarded":"PhD","date_published":"2013-09-05T00:00:00Z","author":[{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736","first_name":"Damien"}],"article_processing_charge":"No","related_material":{"record":[{"id":"2847","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"3251"},{"id":"4361","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:1405","date_updated":"2023-09-07T11:36:37Z","file_date_updated":"2021-11-17T13:47:58Z","citation":{"ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria.","mla":"Zufferey, Damien. <i>Analysis of Dynamic Message Passing Programs</i>. Institute of Science and Technology Austria, 2013, doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>.","short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>.","apa":"Zufferey, D. (2013). <i>Analysis of dynamic message passing programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>"},"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","oa":1,"status":"public","supervisor":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"_id":"1405","year":"2013","has_accepted_license":"1","page":"134","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","abstract":[{"text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point.","lang":"eng"}],"ec_funded":1,"date_created":"2018-12-11T11:51:50Z","oa_version":"Published Version","publist_id":"5802","title":"Analysis of dynamic message passing programs","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria"},{"date_created":"2018-12-11T11:51:50Z","oa_version":"None","publist_id":"5801","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading."}],"date_published":"2013-10-01T00:00:00Z","author":[{"last_name":"Campinho","orcid":"0000-0002-8526-5416","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","full_name":"Campinho, Pedro"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T11:36:07Z","_id":"1406","supervisor":[{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"year":"2013","publication_status":"published","page":"123","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","citation":{"short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013."},"month":"10","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"status":"public","day":"01"},{"abstract":[{"lang":"eng","text":"A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia."}],"extern":1,"quality_controlled":0,"date_published":"2013-09-01T00:00:00Z","author":[{"full_name":"Arkhipov, Vladimir Y","first_name":"Vladimir","last_name":"Arkhipov"},{"first_name":"T","last_name":"Noah","full_name":"Noah T"},{"full_name":"Koschkar, Steffen","first_name":"Steffen","last_name":"Koschkar"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"date_updated":"2021-01-12T08:21:48Z","date_created":"2018-12-11T11:49:07Z","publist_id":"6741","title":"Birds of Mys Shmidta, north Chukotka, Russia","publication":"Forktail","publisher":"Oriental Bird Club","citation":{"ieee":"V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” <i>Forktail</i>, no. 29. Oriental Bird Club, pp. 25–30, 2013.","chicago":"Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” <i>Forktail</i>. Oriental Bird Club, 2013.","apa":"Arkhipov, V., Noah, T., Koschkar, S., &#38; Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. <i>Forktail</i>. Oriental Bird Club.","ama":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. <i>Forktail</i>. 2013;(29):25-30.","mla":"Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” <i>Forktail</i>, no. 29, Oriental Bird Club, 2013, pp. 25–30.","short":"V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.","ista":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30."},"month":"09","status":"public","oa":1,"acknowledgement":"We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper  conservation  programme  in  2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia.","day":"01","issue":"29","main_file_link":[{"open_access":"1","url":"http://orientalbirdclub.org/forktail29/"}],"_id":"905","publication_status":"published","year":"2013","page":"25 - 30","type":"journal_article"},{"citation":{"short":"J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940.","ista":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940.","mla":"Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” <i>Science</i>, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:<a href=\"https://doi.org/10.1126/science.1230020\">10.1126/science.1230020</a>.","ama":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. <i>Science</i>. 2013;339(6122):936-940. doi:<a href=\"https://doi.org/10.1126/science.1230020\">10.1126/science.1230020</a>","apa":"Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., &#38; Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. <i>Science</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/science.1230020\">https://doi.org/10.1126/science.1230020</a>","ieee":"J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” <i>Science</i>, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.","chicago":"Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” <i>Science</i>. American Association for the Advancement of Science , 2013. <a href=\"https://doi.org/10.1126/science.1230020\">https://doi.org/10.1126/science.1230020</a>."},"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"status":"public","issue":"6122","article_type":"original","external_id":{"pmid":["23371555"]},"_id":"9055","year":"2013","volume":339,"page":"936-940","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"text":"Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional \"living crystals,\" which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles.","lang":"eng"}],"extern":"1","date_created":"2021-02-01T14:37:29Z","oa_version":"None","publication":"Science","title":"Living crystals of light-activated colloidal surfers","publisher":"American Association for the Advancement of Science ","month":"02","language":[{"iso":"eng"}],"pmid":1,"day":"22","intvolume":"       339","publication_status":"published","keyword":["Multidisciplinary"],"scopus_import":"1","quality_controlled":"1","author":[{"orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"full_name":"Sacanna, S.","last_name":"Sacanna","first_name":"S."},{"last_name":"Steinberg","first_name":"A. P.","full_name":"Steinberg, A. P."},{"first_name":"D. J.","last_name":"Pine","full_name":"Pine, D. J."},{"first_name":"P. M.","last_name":"Chaikin","full_name":"Chaikin, P. M."}],"date_published":"2013-02-22T00:00:00Z","article_processing_charge":"No","date_updated":"2022-08-25T14:57:43Z","doi":"10.1126/science.1230020"},{"article_processing_charge":"No","date_updated":"2022-01-24T13:46:15Z","doi":"10.1002/2013jc009212","author":[{"first_name":"Angélique","last_name":"Melet","full_name":"Melet, Angélique"},{"last_name":"Nikurashin","first_name":"Maxim","full_name":"Nikurashin, Maxim"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"},{"full_name":"Falahat, S.","first_name":"S.","last_name":"Falahat"},{"full_name":"Nycander, Jonas","last_name":"Nycander","first_name":"Jonas"},{"full_name":"Timko, Patrick G.","first_name":"Patrick G.","last_name":"Timko"},{"full_name":"Arbic, Brian K.","last_name":"Arbic","first_name":"Brian K."},{"full_name":"Goff, John A.","last_name":"Goff","first_name":"John A."}],"date_published":"2013-11-07T00:00:00Z","quality_controlled":"1","day":"07","month":"11","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2013JC009212"}],"extern":"1","abstract":[{"lang":"eng","text":"Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges."}],"publisher":"American Geophysical Union","publication":"Journal of Geophysical Research: Oceans","title":"Internal tide generation by abyssal hills using analytical theory","date_created":"2021-02-15T15:11:39Z","oa_version":"Published Version","issue":"11","article_type":"original","status":"public","oa":1,"publication_identifier":{"issn":["2169-9275"]},"citation":{"ama":"Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal hills using analytical theory. <i>Journal of Geophysical Research: Oceans</i>. 2013;118(11):6303-6318. doi:<a href=\"https://doi.org/10.1002/2013jc009212\">10.1002/2013jc009212</a>","short":"A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko, B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.","ista":"Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.","mla":"Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” <i>Journal of Geophysical Research: Oceans</i>, vol. 118, no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:<a href=\"https://doi.org/10.1002/2013jc009212\">10.1002/2013jc009212</a>.","chicago":"Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2013. <a href=\"https://doi.org/10.1002/2013jc009212\">https://doi.org/10.1002/2013jc009212</a>.","ieee":"A. Melet <i>et al.</i>, “Internal tide generation by abyssal hills using analytical theory,” <i>Journal of Geophysical Research: Oceans</i>, vol. 118, no. 11. American Geophysical Union, pp. 6303–6318, 2013.","apa":"Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko, P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical theory. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2013jc009212\">https://doi.org/10.1002/2013jc009212</a>"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":118,"page":"6303-6318","year":"2013","_id":"9153"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":26,"page":"5028-5043","year":"2013","_id":"9154","issue":"14","article_type":"original","oa":1,"status":"public","publication_identifier":{"issn":["0894-8755","1520-0442"]},"citation":{"ieee":"C. J. Muller, “Impact of convective organization on the response of tropical precipitation extremes to warming,” <i>Journal of Climate</i>, vol. 26, no. 14. American Meteorological Society, pp. 5028–5043, 2013.","chicago":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” <i>Journal of Climate</i>. American Meteorological Society, 2013. <a href=\"https://doi.org/10.1175/jcli-d-12-00655.1\">https://doi.org/10.1175/jcli-d-12-00655.1</a>.","apa":"Muller, C. J. (2013). Impact of convective organization on the response of tropical precipitation extremes to warming. <i>Journal of Climate</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/jcli-d-12-00655.1\">https://doi.org/10.1175/jcli-d-12-00655.1</a>","ama":"Muller CJ. Impact of convective organization on the response of tropical precipitation extremes to warming. <i>Journal of Climate</i>. 2013;26(14):5028-5043. doi:<a href=\"https://doi.org/10.1175/jcli-d-12-00655.1\">10.1175/jcli-d-12-00655.1</a>","ista":"Muller CJ. 2013. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043.","short":"C.J. Muller, Journal of Climate 26 (2013) 5028–5043.","mla":"Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” <i>Journal of Climate</i>, vol. 26, no. 14, American Meteorological Society, 2013, pp. 5028–43, doi:<a href=\"https://doi.org/10.1175/jcli-d-12-00655.1\">10.1175/jcli-d-12-00655.1</a>."},"publisher":"American Meteorological Society","publication":"Journal of Climate","title":"Impact of convective organization on the response of tropical precipitation extremes to warming","date_created":"2021-02-15T15:26:39Z","oa_version":"Published Version","extern":"1","abstract":[{"lang":"eng","text":"In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications.\r\nRegardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming."}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/JCLI-D-12-00655.1"}],"intvolume":"        26","day":"15","month":"07","language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2022-01-24T13:46:41Z","doi":"10.1175/jcli-d-12-00655.1","date_published":"2013-07-15T00:00:00Z","author":[{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"}],"quality_controlled":"1","keyword":["Atmospheric Science"]},{"date_published":"2013-10-30T00:00:00Z","author":[{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","first_name":"Jérémie A"},{"full_name":"Sacanna, Stefano","last_name":"Sacanna","first_name":"Stefano"},{"first_name":"Adrian","last_name":"Vatchinsky","full_name":"Vatchinsky, Adrian"},{"full_name":"Chaikin, Paul M.","first_name":"Paul M.","last_name":"Chaikin"},{"first_name":"David J.","last_name":"Pine","full_name":"Pine, David J."}],"date_updated":"2021-02-22T10:10:41Z","doi":"10.1021/ja406090s","article_processing_charge":"No","scopus_import":"1","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"quality_controlled":"1","intvolume":"       135","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.5724"}],"publication_status":"published","pmid":1,"day":"30","language":[{"iso":"eng"}],"month":"10","title":"Photoactivated colloidal dockers for cargo transportation","publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","oa_version":"Preprint","date_created":"2021-02-18T14:31:26Z","arxiv":1,"abstract":[{"lang":"eng","text":"We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems."}],"extern":"1","page":"15978-15981","volume":135,"type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9167","year":"2013","oa":1,"status":"public","external_id":{"arxiv":["1310.5724"],"pmid":["24131488"]},"article_type":"original","issue":"43","citation":{"apa":"Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., &#38; Pine, D. J. (2013). Photoactivated colloidal dockers for cargo transportation. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja406090s\">https://doi.org/10.1021/ja406090s</a>","chicago":"Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin, and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2013. <a href=\"https://doi.org/10.1021/ja406090s\">https://doi.org/10.1021/ja406090s</a>.","ieee":"J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated colloidal dockers for cargo transportation,” <i>Journal of the American Chemical Society</i>, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013.","mla":"Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.” <i>Journal of the American Chemical Society</i>, vol. 135, no. 43, American Chemical Society, 2013, pp. 15978–81, doi:<a href=\"https://doi.org/10.1021/ja406090s\">10.1021/ja406090s</a>.","short":"J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal of the American Chemical Society 135 (2013) 15978–15981.","ista":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 135(43), 15978–15981.","ama":"Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal dockers for cargo transportation. <i>Journal of the American Chemical Society</i>. 2013;135(43):15978-15981. doi:<a href=\"https://doi.org/10.1021/ja406090s\">10.1021/ja406090s</a>"},"publication_identifier":{"issn":["00027863"],"eissn":["15205126"]}},{"year":"2013","publication_status":"published","intvolume":"       110","_id":"921","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":110,"page":"2452 - 2459","month":"02","language":[{"iso":"eng"}],"citation":{"ieee":"M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing,” <i>PNAS</i>, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013.","chicago":"Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1219937110\">https://doi.org/10.1073/pnas.1219937110</a>.","apa":"Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., &#38; Levine, H. (2013). Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1219937110\">https://doi.org/10.1073/pnas.1219937110</a>","ama":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. <i>PNAS</i>. 2013;110(7):2452-2459. doi:<a href=\"https://doi.org/10.1073/pnas.1219937110\">10.1073/pnas.1219937110</a>","ista":"Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 110(7), 2452–2459.","short":"M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013) 2452–2459.","mla":"Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” <i>PNAS</i>, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2452–59, doi:<a href=\"https://doi.org/10.1073/pnas.1219937110\">10.1073/pnas.1219937110</a>."},"issue":"7","day":"12","status":"public","acknowledgement":"This work was supported by National Science Foundation (NSF) Grant DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf Zaritsky. ","publist_id":"6518","date_created":"2018-12-11T11:49:12Z","oa_version":"None","publisher":"National Academy of Sciences","publication":"PNAS","title":"Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing","extern":"1","abstract":[{"lang":"eng","text":"Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters."}],"article_processing_charge":"No","doi":"10.1073/pnas.1219937110","date_updated":"2021-01-12T08:21:55Z","date_published":"2013-02-12T00:00:00Z","author":[{"full_name":"Basan, Markus","first_name":"Markus","last_name":"Basan"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rappel","first_name":"Wouter","full_name":"Rappel, Wouter"},{"full_name":"Levine, Herbert","last_name":"Levine","first_name":"Herbert"}]},{"volume":153,"page":"193-205","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","_id":"9459","year":"2013","oa":1,"status":"public","issue":"1","external_id":{"pmid":["23540698"]},"article_type":"original","citation":{"ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>"},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"publication":"Cell","department":[{"_id":"DaZi"}],"title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","publisher":"Elsevier","date_created":"2021-06-04T12:23:28Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway."}],"extern":"1","intvolume":"       153","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"publication_status":"published","pmid":1,"day":"28","month":"03","language":[{"iso":"eng"}],"date_published":"2013-03-28T00:00:00Z","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"last_name":"Thao","first_name":"Ka","full_name":"Thao, Ka"},{"full_name":"Harmer, Stacey L.","last_name":"Harmer","first_name":"Stacey L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"article_processing_charge":"No","date_updated":"2021-12-14T08:25:35Z","doi":"10.1016/j.cell.2013.02.033","scopus_import":"1","quality_controlled":"1"},{"year":"2013","_id":"9481","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":110,"page":"7934-7939","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"citation":{"ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013."},"issue":"19","external_id":{"pmid":["23613580"]},"article_type":"original","oa":1,"status":"public","date_created":"2021-06-07T07:31:02Z","oa_version":"Published Version","publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"DaZi"}],"title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","extern":"1","abstract":[{"lang":"eng","text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants."}],"publication_status":"published","intvolume":"       110","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1306164110","open_access":"1"}],"month":"05","language":[{"iso":"eng"}],"day":"07","pmid":1,"quality_controlled":"1","keyword":["Multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","doi":"10.1073/pnas.1306164110","date_updated":"2021-12-14T08:26:44Z","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"last_name":"Ruan","first_name":"Randy","full_name":"Ruan, Randy"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"full_name":"Sharma, Rita","first_name":"Rita","last_name":"Sharma"},{"full_name":"Ronald, Pamela C","first_name":"Pamela C","last_name":"Ronald"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_published":"2013-05-07T00:00:00Z"},{"day":"11","pmid":1,"language":[{"iso":"eng"}],"month":"02","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2013.01.014","open_access":"1"}],"intvolume":"        24","date_updated":"2023-05-08T11:00:59Z","doi":"10.1016/j.devcel.2013.01.014","article_processing_charge":"No","author":[{"orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"first_name":"Hugh","last_name":"Dickinson","full_name":"Dickinson, Hugh"}],"date_published":"2013-02-11T00:00:00Z","quality_controlled":"1","scopus_import":"1","external_id":{"pmid":["23410937"]},"article_type":"review","issue":"3","status":"public","oa":1,"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"citation":{"apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"215-225","volume":24,"year":"2013","_id":"9520","extern":"1","abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"publisher":"Elsevier","title":"A conversation across generations: Soma-germ cell crosstalk in plants","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication":"Developmental Cell","oa_version":"Published Version","date_created":"2021-06-08T06:14:50Z"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","volume":138,"year":"2013","_id":"9663","issue":"16","article_type":"original","external_id":{"pmid":["23635145"]},"status":"public","oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"citation":{"apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>","ieee":"B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16. AIP Publishing, 2013.","chicago":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2013. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>.","short":"B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>.","ista":"Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314.","ama":"Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. 2013;138(16). doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>"},"publisher":"AIP Publishing","publication":"The Journal of Chemical Physics","title":"Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion","date_created":"2021-07-15T09:27:58Z","oa_version":"Submitted Version","extern":"1","abstract":[{"text":"Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity.","lang":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://pubmed.ncbi.nlm.nih.gov/23635145/","open_access":"1"}],"intvolume":"       138","day":"28","pmid":1,"month":"04","language":[{"iso":"eng"}],"article_number":"164314","article_processing_charge":"No","date_updated":"2021-08-09T12:35:34Z","doi":"10.1063/1.4802025","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Ngan, Alfonso H. W.","first_name":"Alfonso H. W.","last_name":"Ngan"}],"date_published":"2013-04-28T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"oa_version":"None","date_created":"2021-07-15T14:27:44Z","title":"The crystal structures of sintered copper nanoparticles: A molecular dynamics study","publication":"International Journal of Plasticity","publisher":"Elsevier","abstract":[{"text":"The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before.","lang":"eng"}],"scopus_import":"1","quality_controlled":"1","extern":"1","date_published":"2013-08-01T00:00:00Z","author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"full_name":"Ngan, Alfonso H.W.","last_name":"Ngan","first_name":"Alfonso H.W."}],"doi":"10.1016/j.ijplas.2013.01.006","date_updated":"2023-02-23T14:04:30Z","article_processing_charge":"No","_id":"9674","intvolume":"        47","publication_status":"published","year":"2013","page":"65-79","volume":47,"type":"journal_article","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79.","ista":"Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 47, 65–79.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” <i>International Journal of Plasticity</i>, vol. 47, Elsevier, 2013, pp. 65–79, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">10.1016/j.ijplas.2013.01.006</a>.","ama":"Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. <i>International Journal of Plasticity</i>. 2013;47:65-79. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">10.1016/j.ijplas.2013.01.006</a>","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). The crystal structures of sintered copper nanoparticles: A molecular dynamics study. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">https://doi.org/10.1016/j.ijplas.2013.01.006</a>","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” <i>International Journal of Plasticity</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.ijplas.2013.01.006\">https://doi.org/10.1016/j.ijplas.2013.01.006</a>.","ieee":"B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles: A molecular dynamics study,” <i>International Journal of Plasticity</i>, vol. 47. Elsevier, pp. 65–79, 2013."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0749-6419"]},"month":"08","status":"public","article_type":"original","day":"01"},{"oa_version":"None","date_created":"2021-07-16T06:46:38Z","publisher":"Elsevier","title":"The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study","publication":"Computational Materials Science","quality_controlled":"1","extern":"1","abstract":[{"lang":"eng","text":"Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses."}],"scopus_import":"1","doi":"10.1016/j.commatsci.2013.03.014","date_updated":"2023-02-23T14:04:35Z","article_processing_charge":"No","author":[{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"},{"last_name":"Ngan","first_name":"Alfonso H.W.","full_name":"Ngan, Alfonso H.W."}],"date_published":"2013-06-01T00:00:00Z","publication_status":"published","year":"2013","intvolume":"        74","_id":"9676","type":"journal_article","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","page":"1-11","volume":74,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0927-0256"]},"month":"06","citation":{"ama":"Cheng B, Ngan AHW. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. <i>Computational Materials Science</i>. 2013;74:1-11. doi:<a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">10.1016/j.commatsci.2013.03.014</a>","ista":"Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 74, 1–11.","short":"B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” <i>Computational Materials Science</i>, vol. 74, Elsevier, 2013, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">10.1016/j.commatsci.2013.03.014</a>.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” <i>Computational Materials Science</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">https://doi.org/10.1016/j.commatsci.2013.03.014</a>.","ieee":"B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study,” <i>Computational Materials Science</i>, vol. 74. Elsevier, pp. 1–11, 2013.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. <i>Computational Materials Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.commatsci.2013.03.014\">https://doi.org/10.1016/j.commatsci.2013.03.014</a>"},"article_type":"original","day":"01","status":"public"},{"year":"2013","publication_status":"published","_id":"9682","intvolume":"       585","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","volume":585,"page":"326-334","month":"11","publication_identifier":{"issn":["0921-5093"]},"language":[{"iso":"eng"}],"citation":{"ista":"Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 585, 326–334.","short":"B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” <i>Materials Science and Engineering: A</i>, vol. 585, Elsevier, 2013, pp. 326–34, doi:<a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">10.1016/j.msea.2013.07.065</a>.","ama":"Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision. <i>Materials Science and Engineering: A</i>. 2013;585:326-334. doi:<a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">10.1016/j.msea.2013.07.065</a>","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals during collision. <i>Materials Science and Engineering: A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">https://doi.org/10.1016/j.msea.2013.07.065</a>","ieee":"B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during collision,” <i>Materials Science and Engineering: A</i>, vol. 585. Elsevier, pp. 326–334, 2013.","chicago":"Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” <i>Materials Science and Engineering: A</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.msea.2013.07.065\">https://doi.org/10.1016/j.msea.2013.07.065</a>."},"article_type":"original","day":"15","status":"public","date_created":"2021-07-19T09:04:36Z","oa_version":"None","publisher":"Elsevier","publication":"Materials Science and Engineering: A","title":"Crystal plasticity of Cu nanocrystals during collision","extern":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation."}],"scopus_import":"1","article_processing_charge":"No","doi":"10.1016/j.msea.2013.07.065","date_updated":"2023-02-23T14:04:51Z","author":[{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Ngan, Alfonso H.W.","last_name":"Ngan","first_name":"Alfonso H.W."}],"date_published":"2013-11-15T00:00:00Z"},{"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":111,"year":"2013","_id":"10384","external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"article_type":"original","issue":"24","status":"public","oa":1,"acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. 2013;111(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>","ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702.","mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>.","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” <i>Physical Review Letters</i>, vol. 111, no. 24. American Physical Society, 2013.","chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>.","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., &#38; Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>"},"publisher":"American Physical Society","title":"Living clusters and crystals from low-density suspensions of active colloids","publication":"Physical Review Letters","oa_version":"Preprint","date_created":"2021-11-29T13:29:31Z","arxiv":1,"extern":"1","abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"publication_status":"published","intvolume":"       111","main_file_link":[{"url":"https://arxiv.org/abs/1311.4681","open_access":"1"}],"day":"11","pmid":1,"language":[{"iso":"eng"}],"month":"12","article_number":"245702","date_updated":"2021-11-29T14:05:19Z","doi":"10.1103/physrevlett.111.245702","article_processing_charge":"No","author":[{"full_name":"Mognetti, B. M.","last_name":"Mognetti","first_name":"B. M."},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Angioletti-Uberti, S.","first_name":"S.","last_name":"Angioletti-Uberti"},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"},{"full_name":"Valeriani, C.","first_name":"C.","last_name":"Valeriani"},{"first_name":"D.","last_name":"Frenkel","full_name":"Frenkel, D."}],"date_published":"2013-12-11T00:00:00Z","quality_controlled":"1","scopus_import":"1","keyword":["general physics and astronomy"]},{"author":[{"first_name":"Joseph A.","last_name":"Napoli","full_name":"Napoli, Joseph A."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"date_published":"2013-08-08T00:00:00Z","article_processing_charge":"No","doi":"10.1039/c3sm51495a","date_updated":"2021-11-29T14:05:23Z","keyword":["condensed matter physics","general chemistry"],"scopus_import":"1","quality_controlled":"1","intvolume":"         9","publication_status":"published","day":"08","month":"08","language":[{"iso":"eng"}],"publication":"Soft Matter","title":"Collapsing nanoparticle-laden nanotubes","publisher":"Royal Society of Chemistry","date_created":"2021-11-29T13:31:24Z","oa_version":"None","abstract":[{"text":"We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.","lang":"eng"}],"extern":"1","volume":9,"page":"8881-8886","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","_id":"10385","year":"2013","acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","status":"public","issue":"37","article_type":"original","citation":{"apa":"Napoli, J. A., Šarić, A., &#38; Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” <i>Soft Matter</i>, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>.","ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>.","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. 2013;9(37):8881-8886. doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>"},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]}},{"publication":"Soft Matter","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","publisher":"Royal Society of Chemistry","date_created":"2021-11-29T14:06:32Z","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface."}],"extern":"1","volume":9,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","_id":"10386","year":"2013","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject.","status":"public","issue":"29","article_type":"original","citation":{"ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” <i>Soft Matter</i>, vol. 9, no. 29. Royal Society of Chemistry, 2013.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>","ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. 2013;9(29). doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>.","short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"article_number":"6677","date_published":"2013-05-03T00:00:00Z","author":[{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Angelo","last_name":"Cacciuto","full_name":"Cacciuto, Angelo"}],"article_processing_charge":"No","date_updated":"2021-11-29T14:29:31Z","doi":"10.1039/c3sm50188d","keyword":["condensed matter physics","general chemistry"],"scopus_import":"1","quality_controlled":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"intvolume":"         9","publication_status":"published","day":"03","month":"05","language":[{"iso":"eng"}]},{"volume":58,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10396","year":"2013","has_accepted_license":"1","status":"public","oa":1,"external_id":{"pmid":["24042795"]},"article_type":"original","issue":"SI-1-Track-G","citation":{"apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>"},"publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"department":[{"_id":"PeJo"}],"title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","publication":"Biomedical Engineering / Biomedizinische Technik","publisher":"De Gruyter","oa_version":"Submitted Version","date_created":"2021-12-01T14:35:35Z","abstract":[{"lang":"eng","text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable."}],"intvolume":"        58","publication_status":"published","file":[{"success":1,"date_created":"2021-12-01T14:38:08Z","content_type":"application/pdf","creator":"schloegl","access_level":"open_access","relation":"main_file","file_name":"Schloegl_Abstract-BMT2013.pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","file_size":149825,"file_id":"10397","date_updated":"2021-12-01T14:38:08Z"}],"pmid":1,"day":"01","ddc":["005","610"],"language":[{"iso":"eng"}],"month":"08","file_date_updated":"2021-12-01T14:38:08Z","article_number":"000010151520134181","conference":{"location":"Graz, Austria","start_date":"2013-09-19","name":"BMT: Biomedizinische Technik ","end_date":"2013-09-21"},"author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"full_name":"Schmidt-Hieber, C.","last_name":"Schmidt-Hieber","first_name":"C."},{"full_name":"Guzman, S. J.","last_name":"Guzman","first_name":"S. J."}],"date_published":"2013-08-01T00:00:00Z","doi":"10.1515/bmt-2013-4181","date_updated":"2021-12-02T12:51:12Z","article_processing_charge":"No","keyword":["biomedical engineering","data analysis","free software"],"quality_controlled":"1"}]