The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

Jonathan P.K. Doye; Hannah Fowler; Domen Prešern; Joakim Bohlin; Lorenzo Rovigatti; Flavio Romano; Petr Šulc; Chak Kui Wong; Ard A. Louis; John S. Schreck; Megan C. Engel; Michael Matthies; Erik Benson; Erik Poppleton; Benedict E.K. Snodin

doi:10.1007/978-1-0716-3028-0_6

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

Jonathan P.K. Doye, Hannah Fowler, Domen Prešern, Joakim Bohlin, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Chak Kui Wong, Ard A. Louis, John S. Schreck, Megan C. Engel, Michael Matthies, Erik Benson, Erik Poppleton, Benedict E.K. Snodin

Machine Integration and Learning for Earth Systems

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

15 Scopus citations

Abstract

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	93-112
Number of pages	20
DOIs	https://doi.org/10.1007/978-1-0716-3028-0_6
State	Published - 2023

Publication series

Name	Methods in Molecular Biology
Volume	2639
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

Coarse-grained models
DNA origami
Molecular simulation

Access to Document

10.1007/978-1-0716-3028-0_6

Cite this

Doye, J. P. K., Fowler, H., Prešern, D., Bohlin, J., Rovigatti, L., Romano, F., Šulc, P., Wong, C. K., Louis, A. A., Schreck, J. S., Engel, M. C., Matthies, M., Benson, E., Poppleton, E., & Snodin, B. E. K. (2023). The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami. In Methods in Molecular Biology (pp. 93-112). (Methods in Molecular Biology; Vol. 2639). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-3028-0_6

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title = "The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami",

abstract = "This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.",

keywords = "Coarse-grained models, DNA origami, Molecular simulation",

author = "Doye, \{Jonathan P.K.\} and Hannah Fowler and Domen Pre{\v s}ern and Joakim Bohlin and Lorenzo Rovigatti and Flavio Romano and Petr {\v S}ulc and Wong, \{Chak Kui\} and Louis, \{Ard A.\} and Schreck, \{John S.\} and Engel, \{Megan C.\} and Michael Matthies and Erik Benson and Erik Poppleton and Snodin, \{Benedict E.K.\}",

note = "Publisher Copyright: {\textcopyright} 2023, Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2023",

doi = "10.1007/978-1-0716-3028-0\_6",

language = "English",

series = "Methods in Molecular Biology",

publisher = "Humana Press Inc.",

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Doye, JPK, Fowler, H, Prešern, D, Bohlin, J, Rovigatti, L, Romano, F, Šulc, P, Wong, CK, Louis, AA, Schreck, JS, Engel, MC, Matthies, M, Benson, E, Poppleton, E & Snodin, BEK 2023, The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2639, Humana Press Inc., pp. 93-112. https://doi.org/10.1007/978-1-0716-3028-0_6

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T1 - The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

AU - Doye, Jonathan P.K.

AU - Fowler, Hannah

AU - Prešern, Domen

AU - Bohlin, Joakim

AU - Rovigatti, Lorenzo

AU - Romano, Flavio

AU - Šulc, Petr

AU - Wong, Chak Kui

AU - Louis, Ard A.

AU - Schreck, John S.

AU - Engel, Megan C.

AU - Matthies, Michael

AU - Benson, Erik

AU - Poppleton, Erik

AU - Snodin, Benedict E.K.

PY - 2023

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N2 - This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

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KW - Coarse-grained models

KW - DNA origami

KW - Molecular simulation

UR - https://www.scopus.com/pages/publications/85159449087

U2 - 10.1007/978-1-0716-3028-0_6

DO - 10.1007/978-1-0716-3028-0_6

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AN - SCOPUS:85159449087

T3 - Methods in Molecular Biology

SP - 93

EP - 112

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

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