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

3 Citations (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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