Literature DB >> 20867621

Markov chain Monte Carlo method without detailed balance.

Hidemaro Suwa1, Synge Todo.   

Abstract

We present a specific algorithm that generally satisfies the balance condition without imposing the detailed balance in the Markov chain Monte Carlo. In our algorithm, the average rejection rate is minimized, and even reduced to zero in many relevant cases. The absence of the detailed balance also introduces a net stochastic flow in a configuration space, which further boosts up the convergence. We demonstrate that the autocorrelation time of the Potts model becomes more than 6 times shorter than that by the conventional Metropolis algorithm. Based on the same concept, a bounce-free worm algorithm for generic quantum spin models is formulated as well.

Mesh:

Year:  2010        PMID: 20867621     DOI: 10.1103/PhysRevLett.105.120603

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  8 in total

Review 1.  Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.

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Journal:  Biophys Rev       Date:  2019-05-21

Review 2.  Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

Authors:  Jinzen Ikebe; Koji Umezawa; Junichi Higo
Journal:  Biophys Rev       Date:  2016-01-11

3.  Bayesian optimization for computationally extensive probability distributions.

Authors:  Ryo Tamura; Koji Hukushima
Journal:  PLoS One       Date:  2018-03-05       Impact factor: 3.240

Review 4.  Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.

Authors:  Hisashi Okumura; Satoru G Itoh
Journal:  Molecules       Date:  2022-04-12       Impact factor: 4.927

5.  Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach.

Authors:  Takuya Mizukami; Shunta Furuzawa; Satoru G Itoh; Saho Segawa; Teikichi Ikura; Kunio Ihara; Hisashi Okumura; Heinrich Roder; Kosuke Maki
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-31       Impact factor: 11.205

6.  Two-dimensional ordering of solute nanoclusters at a close-packed stacking fault: modeling and experimental analysis.

Authors:  Hajime Kimizuka; Shu Kurokawa; Akihiro Yamaguchi; Akira Sakai; Shigenobu Ogata
Journal:  Sci Rep       Date:  2014-12-04       Impact factor: 4.379

Review 7.  Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.

Authors:  Satoru G Itoh; Hisashi Okumura
Journal:  Int J Mol Sci       Date:  2021-02-13       Impact factor: 5.923

Review 8.  Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

Authors:  Shinji Iida; Haruki Nakamura; Junichi Higo
Journal:  Biochem J       Date:  2016-06-15       Impact factor: 3.857

  8 in total

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