A coarse-grained model of DNA nanotube population growth

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 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 behavior of nanotubes 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)
Title of host publicationDNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings
PublisherSpringer Verlag
Pages135-147
Number of pages13
Volume9818
ISBN (Print)9783319439938
DOIs
StatePublished - 2016
Externally publishedYes
Event22nd International Conference on Computing and Molecular Programming, DNA 2016 - Munich, Germany
Duration: Sep 4 2016Sep 8 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9818
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other22nd International Conference on Computing and Molecular Programming, DNA 2016
CountryGermany
CityMunich
Period9/4/169/8/16

Fingerprint

Population Growth
Nanotubes
DNA
Bins
Tile
Ordinary differential equations
Joining
Binning
Coarse-graining
Dynamic models
Polymerization
Nucleation
Fragmentation
Model
Dynamic Behavior
Time-varying
Ordinary differential equation
Polymers
Experiments
Experiment

Keywords

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Mardanlou, V., Green, L. N., Subramanian, H. K. K., Hariadi, R., Kim, J., & Franco, E. (2016). A coarse-grained model of DNA nanotube population growth. In DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings (Vol. 9818, pp. 135-147). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9818). Springer Verlag. https://doi.org/10.1007/978-3-319-43994-5_9

A coarse-grained model of DNA nanotube population growth. / Mardanlou, Vahid; Green, Leopold N.; Subramanian, Hari K K; Hariadi, Rizal; Kim, Jongmin; Franco, Elisa.

DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings. Vol. 9818 Springer Verlag, 2016. p. 135-147 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9818).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mardanlou, V, Green, LN, Subramanian, HKK, Hariadi, R, Kim, J & Franco, E 2016, A coarse-grained model of DNA nanotube population growth. in DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings. vol. 9818, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9818, Springer Verlag, pp. 135-147, 22nd International Conference on Computing and Molecular Programming, DNA 2016, Munich, Germany, 9/4/16. https://doi.org/10.1007/978-3-319-43994-5_9
Mardanlou V, Green LN, Subramanian HKK, Hariadi R, Kim J, Franco E. A coarse-grained model of DNA nanotube population growth. In DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings. Vol. 9818. Springer Verlag. 2016. p. 135-147. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-43994-5_9
Mardanlou, Vahid ; Green, Leopold N. ; Subramanian, Hari K K ; Hariadi, Rizal ; Kim, Jongmin ; Franco, Elisa. / A coarse-grained model of DNA nanotube population growth. DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings. Vol. 9818 Springer Verlag, 2016. pp. 135-147 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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