A coarse-grained model captures the temporal evolution of DNA nanotube length distributions

Vahid Mardanlou, Kimia C. Yaghoubi, Leopold N. Green, Hari K.K. Subramanian, Rizal Hariadi, Jongmin Kim, Elisa Franco

    Research output: Contribution to journalArticle

    1 Citation (Scopus)

    Abstract

    We derive a coarse-grained model that captures the temporal evolution of DNA nanotube length distribution during growth experiments. The model takes into account nucleation, polymerization, joining, and fragmentation processes in the nanotube population. The continuous length distribution is segmented, and the time evolution of the nanotube concentration in each length bin is modeled using ordinary differential equations. The binning choice determines the level of coarse graining. This model can handle time varying concentration of tiles, and we foresee that it will be useful to model dynamic behaviors in other types of biomolecular polymers.

    Original languageEnglish (US)
    Pages (from-to)1-17
    Number of pages17
    JournalNatural Computing
    DOIs
    StateAccepted/In press - Dec 7 2017

    Fingerprint

    Nanotubes
    DNA
    Bins
    Tile
    Ordinary differential equations
    Joining
    Dynamic models
    Nucleation
    Polymerization
    Polymers
    Experiments

    Keywords

    • DNA nanotubes
    • Dynamic DNA nanotechnology
    • Growth
    • Ordinary differential equations

    ASJC Scopus subject areas

    • Computer Science Applications

    Cite this

    Mardanlou, V., Yaghoubi, K. C., Green, L. N., Subramanian, H. K. K., Hariadi, R., Kim, J., & Franco, E. (Accepted/In press). A coarse-grained model captures the temporal evolution of DNA nanotube length distributions. Natural Computing, 1-17. https://doi.org/10.1007/s11047-017-9657-7

    A coarse-grained model captures the temporal evolution of DNA nanotube length distributions. / Mardanlou, Vahid; Yaghoubi, Kimia C.; Green, Leopold N.; Subramanian, Hari K.K.; Hariadi, Rizal; Kim, Jongmin; Franco, Elisa.

    In: Natural Computing, 07.12.2017, p. 1-17.

    Research output: Contribution to journalArticle

    Mardanlou, Vahid ; Yaghoubi, Kimia C. ; Green, Leopold N. ; Subramanian, Hari K.K. ; Hariadi, Rizal ; Kim, Jongmin ; Franco, Elisa. / A coarse-grained model captures the temporal evolution of DNA nanotube length distributions. In: Natural Computing. 2017 ; pp. 1-17.
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