JOPSS - Search Results

Journal Articles

Quasi-boundary based on exchange symmetry theory for multilevel simulations

Shiga, Motoyuki; Masia, M.*

Molecular Simulation, 41(10-12), p.827 - 831, 2014/08

https://doi.org/10.1080/08927022.2014.938068

Times Cited Count：7 Percentile：24.27(Chemistry, Physical)

In this contribution, we propose a novel method (QUEST) which enables the simulation of diffusive systems through QM/MM molecular dynamics. The method is an evolution of BEST, an approach based on imposing a bias potential to hinder exchanges between QM and MM particles. This new method corrects for the main shortcoming of BEST, namely that only static properties could be studied, as the dynamics was disrupted. With QUEST the dynamics is still preserved, albeit at some additional cost in the computation of energy and forces as they are needed for the exchanged configurations between QM and MM particles. Here we describe the theoretical basis of QUEST, and we present the results on a small toy system.

Journal Articles

Inter-atomic force constants from correlation effects among thermal displacement of atoms in PbTe

Xianglian*; Sakuma, Takashi*; Mohapatra, S. R.*; Uehara, Hiroyuki*; Takahashi, Haruyuki*; Kamishima, Osamu*; Igawa, Naoki

Molecular Simulation, 38(5), p.448 - 451, 2012/04

https://doi.org/10.1080/08927022.2011.569547

Times Cited Count：4 Percentile：11.98(Chemistry, Physical)

Diffuse neutron scattering measurements have been performed on powder PbTe at 10 and 294 K. Oscillatory diffuse scattering intensity is clearly observed at 294 K. Oscillatory form of the diffuse neutron scattering intensity for PbTe was explained on inclusion of correlation effects among thermal displacements of atoms. From the values of correlation effects and Debye-Waller temperature parameter, force constants among the first nearest neighboring atoms was calculated, $_{rm Pb-Te}$ = 215 eV/nm $^{2}$ , and the second ones were $_{rm Pb-Pb}$ =108 eV/nm $^{2}$ and $_{rm Te-Te}$ = 144 eV/nm $^{2}$ at 294 K.

Journal Articles

H/D isotope effect on the dihydrogen bond by path integral molecular dynamics simulation

Hayashi, Aiko*; Shiga, Motoyuki; Tachikawa, Masanori*

Molecular Simulation, 33(1-2), p.185 - 188, 2007/02

https://doi.org/10.1080/08927020601052963

Times Cited Count：3 Percentile：8.69(Chemistry, Physical)

Ab initio path integral molecular dynamics simulation has been performed to investigate the lithium-hydrogen bond and dihydrogen bond of CHLiH complex. It has been found from the simulation that these unusual types of hydrogen bonds have large geometrical isotope effect which is similar to that of the conventional hydrogen bonding.

Journal Articles

quantum mechanical/molecular mechanical molecular dynamics using multiple-time-scale approach and perturbation theory

Shiga, Motoyuki; Tachikawa, Masanori*

Molecular Simulation, 33(1-2), p.171 - 184, 2007/02

https://doi.org/10.1080/08927020601052922

Times Cited Count：16 Percentile：48.18(Chemistry, Physical)

A new computational method is proposed for quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) which is limited to time-independent thermodynamic analysis. The idea is to use the mass-scaling method combined with multiple-time-scale algorithm and an approximate QM/MM Hamiltonian derived from the first-order Rayleigh-Schroedinger perturbation theory in which the electronic polarization is neglected as a first approximation. If the polarization effect is not so strong, the correction can also be considered after the simulation run using the weighted sampling method. The advantage and disadvantage of the method is discussed in terms of its computational efficiency and accuracy. As a simple example, we demonstrate an MD simulation of liquid water containing 1 QM molecule and 255 MM molecules, and discuss the advantages in calculating statistical averages such as radial distribution and heat of solution.

Journal Articles

DNA deformability and hydration studied by molecular dynamics simulation

Yonetani, Yoshiteru*; Kono, Hidetoshi; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

Molecular Simulation, 33(1-2), p.103 - 107, 2007/01

https://doi.org/10.1080/08927020601052971

Times Cited Count：5 Percentile：15.85(Chemistry, Physical)

DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics simulations of these two sequences, and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove than the flexible TTAA. The result suggests that the hydration water molecules play a critical role for determining the sequence dependent deformability of DNA conformation.

Journal Articles