DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

Carsten Svaneborg; Harold Fellermann; Steen  Rasmussen

doi:10.1007/978-3-642-32208-2_10

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

Carsten Svaneborg, Harold Fellermann, Steen Rasmussen

Institut for Fysik, Kemi og Farmaci

Publikation: Kapitel i bog/rapport/konference-proceeding › Konferencebidrag i proceedings › Forskning › peer review

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Abstrakt

We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation.

Originalsprog	Engelsk
Titel	DNA Computing and Molecular Programming
Forlag	Springer
Publikationsdato	2012
Sider	123-134
ISBN (Trykt)	978-3-642-32207-5
ISBN (Elektronisk)	978-3-642-32208-2
DOI	https://doi.org/10.1007/978-3-642-32208-2_10
Status	Udgivet - 2012
Begivenhed	International Conference on DNA Computing and Molecular Programming - Århus, Danmark Varighed: 14. aug. 2012 → 17. aug. 2012

Konference

Konference	International Conference on DNA Computing and Molecular Programming
Land/Område	Danmark
By	Århus
Periode	14/08/2012 → 17/08/2012

Navn	Lecture Notes in Computer Science
Vol/bind	7433
ISSN	0302-9743

Dokumenter og links

10.1007/978-3-642-32208-2_10

https://arxiv.org/pdf/1204.0733.pdf

1 Foredrag og præsentationer i privat eller offentlig virksomhed

Dynamic Bonded DNA models
Carsten Svaneborg (Foredragsholder)
15. aug. 2012
Aktivitet: Foredrag og mundtlige bidrag › Foredrag og præsentationer i privat eller offentlig virksomhed

Citationsformater

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title = "DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model",

abstract = "We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation. ",

author = "Carsten Svaneborg and Harold Fellermann and Steen Rasmussen",

year = "2012",

doi = "10.1007/978-3-642-32208-2_10",

language = "English",

isbn = "978-3-642-32207-5",

series = "Lecture Notes in Computer Science",

publisher = "Springer",

pages = "123--134",

booktitle = "DNA Computing and Molecular Programming",

address = "Germany",

note = "International Conference on DNA Computing and Molecular Programming, DNA 2012 ; Conference date: 14-08-2012 Through 17-08-2012",

}

Svaneborg, C, Fellermann, H & Rasmussen, S 2012, DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. i DNA Computing and Molecular Programming. Springer, Lecture Notes in Computer Science, bind 7433, s. 123-134, International Conference on DNA Computing and Molecular Programming, Århus, Danmark, 14/08/2012. https://doi.org/10.1007/978-3-642-32208-2_10

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. / Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen .

DNA Computing and Molecular Programming. Springer, 2012. s. 123-134 (Lecture Notes in Computer Science, Bind 7433).

Publikation: Kapitel i bog/rapport/konference-proceeding › Konferencebidrag i proceedings › Forskning › peer review

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T1 - DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

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AU - Rasmussen, Steen

PY - 2012

Y1 - 2012

N2 - We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation.

AB - We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation.

U2 - 10.1007/978-3-642-32208-2_10

DO - 10.1007/978-3-642-32208-2_10

M3 - Article in proceedings

SN - 978-3-642-32207-5

T3 - Lecture Notes in Computer Science

SP - 123

EP - 134

BT - DNA Computing and Molecular Programming

PB - Springer

T2 - International Conference on DNA Computing and Molecular Programming

Y2 - 14 August 2012 through 17 August 2012

ER -

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

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