Natural Computing

, Volume 17, Issue 1, pp 183–199 | Cite as

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 F. Hariadi
  • Jongmin Kim
  • Elisa Franco


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.


DNA nanotubes Ordinary differential equations Growth Dynamic DNA nanotechnology 



The authors thank Deborah K. Fygenson, Bernard Yurke, Rebecca Schulman, and Martha Grover for advice and discussions. This research was entirely supported by DE Grant SC0010595.


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© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  1. 1.Electrical and Computer EngineeringUniversity of California at RiversideRiversideUSA
  2. 2.NeuroscienceUniversity of California at RiversideRiversideUSA
  3. 3.BioengineeringUniversity of California at RiversideRiversideUSA
  4. 4.Department of Physics and Biodesign InstituteArizona State UniversityTempeUSA
  5. 5.Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonUSA
  6. 6.Mechanical EngineeringUniversity of California at RiversideRiversideUSA

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