ニシモリ　ヒラク   NISHIMORI HIRAKU   西森　拓    所属   明治大学研究・知財戦略機構・農場  研究・知財戦略機構    職種   特任教授
言語種別	英語
発行・発表の年月	2017
形態種別	学術雑誌
査読	査読あり
標題	The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry.
執筆形態	共著(筆頭者以外)
掲載誌名	Frontiers in physiology
掲載区分	国外
巻・号・頁	8,pp.103
著者・共著者	Kameda Takeru, Isami Shuhei, Togashi Yuichi, Nishimori Hiraku, Sakamoto Naoaki, Awazu Akinori
概要	This study proposes coarse-grained elastic network models of DNA, called 1-particle-per-k-nucleotides (1PkN), to analyze the global dynamics of long DNA sequences while accounting for sequence-dependent geometry. These models were calibrated using anisotropic fluctuation data from a previous 1-particle-per-1-nucleotide (1P1N) model, which closely matched all-atom simulations. Among the variants, the 1P3N and 1P4N models effectively capture local dynamics, such as twisting motions. Designed for large-scale structures like 10-nm chromatin fibers or mitochondrial and phage DNA, the models enable efficient analysis with low computational cost. As a demonstration, the study analyzed the physical properties of entire human and Plasmodium falciparum mitochondrial genomes.
DOI	10.3389/fphys.2017.00103
ISSN	1664-042X
PMID	28382002