A coarse-grained model of DNA nanotube population growth

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

doi:10.1007/978-3-319-43994-5_9

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 proceeding › Conference contribution

3 Scopus citations

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 language	English (US)
Title of host publication	DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings
Publisher	Springer Verlag
Pages	135-147
Number of pages	13
Volume	9818
ISBN (Print)	9783319439938
DOIs	https://doi.org/10.1007/978-3-319-43994-5_9
State	Published - 2016
Externally published	Yes
Event	22nd International Conference on Computing and Molecular Programming, DNA 2016 - Munich, Germany Duration: Sep 4 2016 → Sep 8 2016

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9818
ISSN (Print)	03029743
ISSN (Electronic)	16113349

Other

Other	22nd International Conference on Computing and Molecular Programming, DNA 2016
Country/Territory	Germany
City	Munich
Period	9/4/16 → 9/8/16

Keywords

DNA nanotubes
Dynamic DNA nanotechnology
Growth
Ordinary differential equations

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-319-43994-5_9

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 et al.
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 proceeding › Conference 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)). doi: 10.1007/978-3-319-43994-5_9

Mardanlou, Vahid ; Green, Leopold N. ; Subramanian, Hari K K et al. / 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)).

@inproceedings{c7e1f95b2ec14232bc5812a4385ba655,

title = "A coarse-grained model of DNA nanotube population growth",

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.",

keywords = "DNA nanotubes, Dynamic DNA nanotechnology, Growth, Ordinary differential equations",

author = "Vahid Mardanlou and Green, {Leopold N.} and Subramanian, {Hari K K} and Rizal Hariadi and Jongmin Kim and Elisa Franco",

year = "2016",

doi = "10.1007/978-3-319-43994-5_9",

language = "English (US)",

isbn = "9783319439938",

volume = "9818",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "135--147",

booktitle = "DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings",

address = "Germany",

note = "22nd International Conference on Computing and Molecular Programming, DNA 2016 ; Conference date: 04-09-2016 Through 08-09-2016",

}

TY - GEN

T1 - A coarse-grained model of DNA nanotube population growth

AU - Mardanlou, Vahid

AU - Green, Leopold N.

AU - Subramanian, Hari K K

AU - Hariadi, Rizal

AU - Kim, Jongmin

AU - Franco, Elisa

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - DNA nanotubes

KW - Dynamic DNA nanotechnology

KW - Growth

KW - Ordinary differential equations

UR - http://www.scopus.com/inward/record.url?scp=84984871000&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84984871000&partnerID=8YFLogxK

U2 - 10.1007/978-3-319-43994-5_9

DO - 10.1007/978-3-319-43994-5_9

M3 - Conference contribution

AN - SCOPUS:84984871000

SN - 9783319439938

VL - 9818

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 135

EP - 147

BT - DNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings

PB - Springer Verlag

T2 - 22nd International Conference on Computing and Molecular Programming, DNA 2016

Y2 - 4 September 2016 through 8 September 2016

ER -

A coarse-grained model of DNA nanotube population growth

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this