arXiv subjects

Kei Moritsugu

Publications and source records attributed to Kei Moritsugu.

3 recordsLinked to original sources

arXiv2021

Analysis of multiple data sequences with different distributions: defining common principal component axes by ergodic sequence generation and multiple reweighting composition

Principal component analysis (PCA) defines a reduced space described by PC axes for a given multidimensional-data sequence to capture the variations of the data. In practice, we need multiple data sequences that accurately obey individual probability distributions and for a fair comparison of the sequences we need PC axes that are common for the multiple sequences but properly capture these multiple distributions. For these requirements, we present individual ergodic samplings for these sequences and provide special reweighting for recovering the target distributions.

stat.ME↗

arXiv2020

On ergodicity for multi-dimensional harmonic oscillator systems with Nose-Hoover type thermostat

A simple proof and detailed analysis on the non-ergodicity for multidimensional harmonic oscillator systems with Nose-Hoover type thermostat are given. The origin of the nonergodicity is symmetries in the multidimensional target physical system, and is differ from that in the Nose-Hoover thermostat with the 1-dimensional harmonic oscillator. A new simple deterministic method to recover the ergodicity is also presented. An individual thermostat variable is attached to each degree of freedom, and all these variables act on a friction coefficient for each degree of freedom. This action is linear and controlled by a Nosé mass matrix Q, which is a matrix analogue of the scalar Nosé's mass. Matrix Q can break the symmetry and contribute to attain the ergodicity.

nlin.CD↗

arXiv2013

Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer

We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling (MSES) technique suggested by Moritsugu and coworkers (J. Chem. Phys. 133, 224105 (2010)). The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and computed more efficiently than the original system. We simulate this combined system (original + CG system) using (underdamped) Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and able to sample the configuration and path space more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange where we prepare many path replica with different coupling strengths. As a result, an unbiased path ensemble for the original system can be found in the weakest coupling path ensemble. This strategy is easily implemented because a weight for a path calculated by the OM action is formally the same as the Boltzmann weight if we properly define the path "Hamiltonian". We apply this method to a model polymer with Asakura-Oosawa interaction, and compare the results with the conventional transition path sampling method.

physics.bio-ph↗