Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

Shuhei Isami; Naoaki Sakamoto; Hiraku Nishimori; Akinori Awazu

doi:10.1371/journal.pone.0143760

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Open Access

Peer-reviewed

Research Article

Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

Shuhei Isami,

Affiliation Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
⨯
Naoaki Sakamoto,

Affiliations Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
⨯
Hiraku Nishimori,

Affiliations Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
⨯
Akinori Awazu

* E-mail: awa@hiroshima-u.ac.jp

Affiliations Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
⨯

Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

Shuhei Isami,
Naoaki Sakamoto,
Hiraku Nishimori,
Akinori Awazu

Published: December 1, 2015
https://doi.org/10.1371/journal.pone.0143760

About the Authors

Shuhei Isami

Affiliation Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan

Naoaki Sakamoto

Affiliations Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan, Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan

Hiraku Nishimori

Akinori Awazu

* E-mail: awa@hiroshima-u.ac.jp

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: AA NS. Performed the experiments: SI AA. Analyzed the data: SI AA. Wrote the paper: AA NS HN.

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Crystal structure
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Nucleotides
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DNA structure
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Network analysis
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Elasticity
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Nucleotide sequencing
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Molecular dynamics
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Biochemical simulations
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