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Featured researches published by Nobu C. Shirai.


arXiv: Statistical Mechanics | 2013

Multicanonical simulation of the Domb-Joyce model and the Gō model: new enumeration methods for self-avoiding walks

Nobu C. Shirai; Macoto Kikuchi

We develop statistical enumeration methods for self-avoiding walks using a powerful sampling technique called the multicanonical Monte Carlo method. Using these methods, we estimate the numbers of the two dimensional N-step self-avoiding walks up to N = 256 with statistical errors. The developed methods are based on statistical mechanical models of paths which include self-avoiding walks. The criterion for selecting a suitable model for enumerating self-avoiding walks is whether or not the configuration space of the model includes a set for which the number of the elements can be exactly counted. We call this set a scale fixing set. We selected the following two models which satisfy the criterion: the Gō model for lattice proteins and the Domb-Joyce model for generalized random walks. There is a contrast between these two models in the structures of the configuration space. The configuration space of the Gō model is defined as the universal set of self-avoiding walks, and the set of the ground state conformation provides a scale fixing set. On the other hand, the configuration space of the Domb-Joyce model is defined as the universal set of random walks which can be used as a scale fixing set, and the set of the ground state conformation is the same as the universal set of self-avoiding walks. From the perspective of enumeration performance, we conclude that the Domb-Joyce model is the better of the two. The reason for the performance difference is partly explained by the existence of the first-order phase transition of the Gō model.


Interdisciplinary Information Sciences | 2013

How to Estimate the Number of Self-Avoiding Walks over 10100? Use Random Walks

Nobu C. Shirai; Macoto Kikuchi

Counting the number of N-step self-avoiding walks (SAWs) on a lattice is one of the most difficult problems of enumerative combinatorics. Once we give up calculating the exact number of them, however, we have a chance to apply powerful computational methods of statistical mechanics to this problem. In this paper, we develop a statistical enumeration method for SAWs using the multicanonical Monte Carlo method. A key part of this method is to expand the configuration space of SAWs to random walks, the exact number of which is known. Using this method, we estimate a number of N-step SAWs on a square lattice, c_N, up to N=256. The value of c_256 is 5.6(1)*10^108 (the number in the parentheses is the statistical error of the last digit) and this is larger than one googol (10^100).


Journal of Chemical Physics | 2013

Structural flexibility of intrinsically disordered proteins induces stepwise target recognition

Nobu C. Shirai; Macoto Kikuchi


Biophysical Journal | 2018

Funnel GAS Model for Protein Many-Body Systems under the Crowded Environment

Macoto Kikuchi; Yoshikatsu Tada; Nobu C. Shirai


生物物理 | 2014

3P118 クロマトソームの粗視化シミュレーション : H1結合に伴うヌクレオソーム構造のコンパクト化のダイナミクス(04. 核酸結合蛋白質,ポスター,第52回日本生物物理学会年会(2014年度))

Nobu C. Shirai; Shoji Takada


Seibutsu Butsuri | 2014

3P118 Coarse-grained simulation of chromatosome : H1-mediated dynamic compaction of nucleosome structure(04. Nucleic acid binding proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Nobu C. Shirai; Shoji Takada


Archive | 2014

Interplay of intrinsic disorder and macromolecular crowding on fibril formation of {\alpha}-synuclein

Nobu C. Shirai; Macoto Kikuchi


生物物理 | 2013

2P074 α-シヌクレイン繊維形成に対する分子混雑の影響(01D.蛋白質:機能,ポスター,日本生物物理学会年会第51回(2013年度))

Nobu C. Shirai; Macoto Kikuchi


Seibutsu Butsuri | 2013

2P074 Macromolecular crowding effect on fibril formation of α-synuclein(01D. Protein: Function,Poster)

Nobu C. Shirai; Macoto Kikuchi


生物物理 | 2012

1B1534 天然変性タンパク質の構造ゆらぎを生かした密度変化誘起型シグナル伝達過程(蛋白質-構造機能相関I,口頭発表,日本生物物理学会第50回年会(2012年度))

Nobu C. Shirai; Macoto Kikuchi

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