@inproceedings{
    CzOr13_orponen,
    editor = "Dediu, A.-H. and Martin-Vide, C. and Truthe, B. and Vega-Rodriguez, M. A.",
    author = "Czeizler, Eugen and Orponen, Pekka",
    isbn = "978-3-642-45007-5",
    series = "Lecture Notes in Computer Science",
    abstract = "The staged Tile Assembly Model has been introduced by Demaine et al. 2008 as an enhancement of the previous tile self-assembly model of Winfree. In this framework, the assembly is allowed to be performed in parallel in different test-tubes, and the obtained products are stored and mixed in subsequent assembly stages. Using elegant combinatorial constructions, in has been shown that staged assembly systems possess remarkable advantage in comparison to their abstract counterparts. Because of their parallel nature, one can choose from a multitude of staged assembly strategies for assembling a given target structure. In the current work we analyze these assembly variations from a kinetic perspective, in order to determine and possibly maximize, their final assembly yield. As a pre-requirement for this task, we provide a procedure for associating an analytically tractable mathematical model to a given staged assembly experiment, based on which we can predict the yield concentration of the final assembly product. As a case study, we consider various assembly strategies as well as optimized and non-optimized assembly protocols for generating a size-10 tile assembly.",
    il = "no",
    eventdetails = "2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013), C\'aceres, Spain, 3-5 December 2013",
    year = "2013",
    keywords = "Tile Assembly Model, staged assembly, numerical modelling, yield optimisation",
    juforank = "1",
    title = "Yield optimization strategies for {DNA} staged tile assembly systems",
    booktitle = "Proceedings of the 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013, C\'aceres, Spain, Dec 2013)",
    note = "",
    unitcode = "T306-99, T312-1",
    impactfactor = "A4",
    responsibleauthor = "Czeizler, Eugen and Orponen, Pekka",
    volume = "8273",
    address = "Berlin Heidelberg",
    kay = "NA",
    pages = "31--44",
    publisher = "Springer-Verlag",
    doi = "10.1007/978-3-642-45008-2_3",
    language = "eng",
    url = "",
    country = "Germany",
    flags = "public HIIT"
}