title: The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry.
abstract: Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle representsknucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human andPlasmodium falciparumgenomes.
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University Hiroshima, Japan.
authors.forename: Takeru
authors.initials: T
authors.lastname: Kameda
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University Hiroshima, Japan.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Isami
authors.affiliation: Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University Hiroshima, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Togashi
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan.
authors.forename: Hiraku
authors.initials: H
authors.lastname: Nishimori
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Sakamoto
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima UniversityHiroshima, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima UniversityHiroshima, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Awazu
keywords: coarse-grained; double-stranded DNA; elastic network model; mitochondrial DNA; normal-mode analysis; sequence-dependent geometry