Hisashi Okumura

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Molecular dynamics simulations are performed to investigate the microscopic dynamics of a bubble when liquids are locally heated. We successfully observe that the heated atoms scatter the neighboring nonheated atoms and make a bubble, and then the bubble is cooled and compressed by the surrounding liquids. The bubble dynamics in this process agrees with the(More)
We applied the multibaric-multithermal (MUBATH) molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of conformational space and sampled the states of PII, C5, alphaR, alphaP, alphaL, and C7(ax). On the other hand, the conventional isobaric-isothermal simulation was trapped in(More)
We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The(More)
We present three generalized isobaric-isothermal ensemble Monte Carlo algorithms, which we refer to as the multibaric-multithermal, multibaric-isothermal, and isobaric-multithermal algorithms. These Monte Carlo simulations perform random walks widely in volume space and/or in potential energy space. From only one simulation run, one can calculate(More)
We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this(More)
Chitosan is an important biopolymer in the medical applications because of its excellent biocompatibility. It has been recently highlighted in the targeted drug delivery system (DDS) by improvement of the carbon nanotube (CNT) solubility. To investigate the effect of chitosan length, the two targeted DDSs with 30 and 60 chitosan monomers were performed by(More)
The use of the replica exchange (RE) molecular dynamics (MD) method for the efficient estimation of conformational populations of ligand-sized molecules in solution is investigated. We compare the computational efficiency of the traditional constant temperature MD technique with that of the parallel RE molecular dynamics method for a series of alkanes and(More)
Pain is a harmful sensation that arises from noxious stimuli. Transient receptor potential ankyrin 1 (TRPA1) is one target for studying pain mechanisms. TRPA1 is activated by various stimuli such as noxious cold, pungent natural products and environmental irritants. Since TRPA1 is an attractive target for pain therapy, a few TRPA1 antagonists have been(More)
We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges,(More)
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM). In RPM, not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the(More)