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Research Output 1994 2019

  • 3917 Citations
  • 36 h-Index
  • 195 Article
  • 13 Conference contribution
  • 8 Chapter
  • 1 Conference article
2019

Anisotropy of dodecahedral water cages for guest gas occupancy in semiclathrate hydrates

Yuhara, D., Yasuoka, K., Takeya, S. & Muromachi, S., 2019 Jan 1, In : Chemical Communications. 55, 68, p. 10150-10153 4 p.

Research output: Contribution to journalArticle

Hydrates
Anisotropy
Gases
Noble Gases
Water
3 Citations (Scopus)

Cage occupancies, lattice constants, and guest chemical potentials for structure II hydrogen clathrate hydrate from Gibbs ensemble Monte Carlo simulations

Brumby, P. E., Yuhara, D., Hasegawa, T., Wu, D. T., Sum, A. K. & Yasuoka, K., 2019 Apr 7, In : Journal of Chemical Physics. 150, 13, 134503.

Research output: Contribution to journalArticle

Chemical potential
clathrates
Hydrates
hydrates
Lattice constants

Detection of molecular behavior that characterizes systems using a deep learning approach

Endo, K., Yuhara, D., Tomobe, K. & Yasuoka, K., 2019 May 28, In : Nanoscale. 11, 20, p. 10064-10071 8 p.

Research output: Contribution to journalArticle

Molecular dynamics
Computational methods
Probability distributions
Physics
Deep learning
Molecular dynamics
Computer simulation
Atoms
Wetting
Liquids

Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

Tomobe, K., Yamamoto, E. & Yasuoka, K., 2019 Jan 1, Methods in Molecular Biology. Humana Press Inc., p. 21-30 10 p. (Methods in Molecular Biology; vol. 1947).

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular Dynamics Simulation
Rhodopsin
Water
G-Protein-Coupled Receptors
Signal Transduction

Ordering in clusters of uniaxial anisotropic particles during homogeneous nucleation and growth

Nozawa, T., Brumby, P. E., Ayuba, S. & Yasuoka, K., 2019 Feb 7, In : Journal of Chemical Physics. 150, 5, 054903.

Research output: Contribution to journalArticle

Nucleation
nucleation
elongation
Elongation
Molecular interactions
Open Access
Carbon Nanotubes
Carbon nanotubes
Alcohols
Electric fields
Water

Separation of water-alcohol mixtures using carbon nanotubes under an electric field

Winarto, W., Yamamoto, E. & Yasuoka, K., 2019 Jan 1, In : Physical Chemistry Chemical Physics. 21, 28, p. 15431-15438 8 p.

Research output: Contribution to journalArticle

Carbon Nanotubes
alcohols
carbon nanotubes
Electric fields
Alcohols
2018
1 Citation (Scopus)

A fast and accurate computational method for the linear-combination-based isotropic periodic sum

Takahashi, K. Z., Nozawa, T. & Yasuoka, K., 2018 Dec 1, In : Scientific Reports. 8, 1, 11880.

Research output: Contribution to journalArticle

Computational methods
Fast Fourier transforms
Computational efficiency
Boundary conditions
Costs
3 Citations (Scopus)

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

Yuhara, D., Brumby, P. E., Wu, D. T., Sum, A. K. & Yasuoka, K., 2018 May 14, In : Journal of Chemical Physics. 148, 18, 184501.

Research output: Contribution to journalArticle

Methane
Hydrates
Phase equilibria
hydrates
Molecular dynamics
2 Citations (Scopus)

Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Nozawa, T., Yasuoka, K. & Takahashi, K. Z., 2018 Dec 1, In : Scientific Reports. 8, 1, 4185.

Research output: Contribution to journalArticle

Atoms
Molecules
5 Citations (Scopus)

Density functional theory study of atomic and electronic properties of defects in reduced anatase TiO2 nanocrystals

Morita, K. & Yasuoka, K., 2018 Mar 1, In : AIP Advances. 8, 3, 035119.

Research output: Contribution to journalArticle

anatase
nanocrystals
density functional theory
defects
electronics

Detection of Anomalous Dynamics for a Single Water Molecule

Tomobe, K. & Yasuoka, K., 2018 Mar 13, In : Journal of Chemical Theory and Computation. 14, 3, p. 1177-1185 9 p.

Research output: Contribution to journalArticle

Molecules
Water
water
molecules
Biological systems
1 Citation (Scopus)

Effect of central longitudinal dipole interactions on chiral liquid-crystal phases

Nozawa, T., Brumby, P. E. & Yasuoka, K., 2018 Sep 11, In : International Journal of Molecular Sciences. 19, 9, 2715.

Research output: Contribution to journalArticle

Liquid Crystals
Phase behavior
Liquid crystals
liquid crystals
dipoles
6 Citations (Scopus)

Kinetic analysis of homogeneous droplet nucleation using large-scale molecular dynamics simulations

Ayuba, S., Suh, D., Nomura, K., Ebisuzaki, T. & Yasuoka, K., 2018 Jul 28, In : Journal of Chemical Physics. 149, 4, 044504.

Research output: Contribution to journalArticle

Molecular dynamics
Nucleation
nucleation
molecular dynamics
Kinetics

Molecular Dynamics Simulation of Ice Crystal Growth Inhibition by Hexadecyl-trimethyl-ammonium Bromide

Shimazu, N., Takaiwa, D., Suh, D., Kawaguchi, T., Fuse, T., Kaneko, T. & Yasuoka, K., 2018 Aug 7, In : Langmuir. 34, 31, p. 9330-9335 6 p.

Research output: Contribution to journalArticle

ammonium bromides
Ice
Crystallization
Crystal growth
Molecular dynamics
1 Citation (Scopus)

Multi-step time series generator for molecular dynamics

Endo, K., Tomobe, K. & Yasuoka, K., 2018 Jan 1, 32nd AAAI Conference on Artificial Intelligence, AAAI 2018. AAAI press, p. 2192-2199 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Molecular dynamics
Time series
Polymer melts
Computational methods
Feature extraction
6 Citations (Scopus)

Oxygen vacancy-originated highly active electrocatalysts for the oxygen evolution reaction

Hirai, S., Morita, K., Yasuoka, K., Shibuya, T., Tojo, Y., Kamihara, Y., Miura, A., Suzuki, H., Ohno, T., Matsuda, T. & Yagi, S., 2018 Jan 1, In : Journal of Materials Chemistry A. 6, 31, p. 15102-15109 8 p.

Research output: Contribution to journalArticle

Electrocatalysts
Oxygen vacancies
Reactive Oxygen Species
Oxygen
Hydrogen fuels
5 Citations (Scopus)

Phase behaviors of deeply supercooled bilayer water unseen in bulk water

Kaneko, T., Bai, J., Akimoto, T., Francisco, J. S., Yasuoka, K. & Zeng, X. C., 2018 May 8, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 19, p. 4839-4844 6 p.

Research output: Contribution to journalArticle

Ice
Water
Isochores
Freezing
Pressure

Recent advances in clathrate hydrates research using molecular simulations

Yuhara, D., Hiratsuka, M. & Yasuoka, K., 2018 Jan 1, In : Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu. 28, 2, p. 102-112 11 p.

Research output: Contribution to journalArticle

clathrates
Hydrates
hydrates
Molecular dynamics
thermodynamic properties

Self-assembly of peptide amphiphiles by vapor pressure osmometry and dissipative particle dynamics

Seki, T., Arai, N., Suh, D., Ozawa, T., Shimada, T., Yasuoka, K. & Hotta, A., 2018 Jan 1, In : RSC Advances. 8, 47, p. 26461-26468 8 p.

Research output: Contribution to journalArticle

Amphiphiles
Vapor pressure
Self assembly
Peptides
Gelation

Structural determinants in the bulk heterojunction

Acocella, A., Höfinger, S., Haunschmid, E., Pop, S. C., Narumi, T., Yasuoka, K., Yasui, M. & Zerbetto, F., 2018 Jan 1, In : Physical Chemistry Chemical Physics. 20, 8, p. 5708-5720 13 p.

Research output: Contribution to journalArticle

solar energy conversion
Energy conversion
determinants
Solar energy
Heterojunctions
4 Citations (Scopus)

Theoretical analyses on water cluster structures in polymer electrolyte membrane by using dissipative particle dynamics simulations with fragment molecular orbital based effective parameters

Okuwaki, K., Mochizuki, Y., Doi, H., Kawada, S., Ozawa, T. & Yasuoka, K., 2018 Jan 1, In : RSC Advances. 8, 60, p. 34582-34595 14 p.

Research output: Contribution to journalArticle

Molecular orbitals
Electrolytes
Polyether ether ketones
Polymers
Membranes
2017
3 Citations (Scopus)

Critical test of bead–spring model to resolve the scaling laws of polymer melts: a molecular dynamics study

Takahashi, K. Z., Yamato, N., Yasuoka, K. & Masubuchi, Y., 2017 Jun 11, (Accepted/In press) In : Molecular Simulation. p. 1-6 6 p.

Research output: Contribution to journalArticle

Polymer Melts
Polymer melts
Scaling laws
Scaling Laws
Molecular Dynamics
6 Citations (Scopus)

Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

Doi, H., Okuwaki, K., Mochizuki, Y., Mochizuki, Y., Ozawa, T. & Yasuoka, K., 2017, In : Chemical Physics Letters. 684, p. 427-432 6 p.

Research output: Contribution to journalArticle

choline
Molecular orbitals
Phosphatidylcholines
molecular orbitals
fragments
17 Citations (Scopus)

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

Yamamoto, E., Akimoto, T., Kalli, A. C., Yasuoka, K. & Sansom, M. S. P., 2017 Jan 1, In : Science advances. 3, 1, e1601871.

Research output: Contribution to journalArticle

Membrane Lipids
Carrier Proteins
Membrane Proteins
Phosphatidylinositol Phosphates
Membranes
3 Citations (Scopus)
monosaccharides
Monosaccharides
Isomers
Hydration
hydration
16 Citations (Scopus)

Evidence of low-density and high-density liquid phases and isochore end point for water confined to carbon nanotube

Nomura, K., Kaneko, T., Bai, J., Francisco, J. S., Yasuoka, K. & Zeng, X. C., 2017 Apr 18, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 16, p. 4066-4071 6 p.

Research output: Contribution to journalArticle

Isochores
Carbon Nanotubes
Ice
Water
Nanotubes
2 Citations (Scopus)

Heterogeneous cavitation and crystallisation with an impurity by molecular dynamics

Suh, D. & Yasuoka, K., 2017 Nov 19, (Accepted/In press) In : Molecular Simulation. p. 1-4 4 p.

Research output: Contribution to journalArticle

Cavitation
Crystallization
cavitation flow
Impurities
Molecular Dynamics
7 Citations (Scopus)

Molecular Dynamics Simulation of Water Nanodroplet Bounce Back from Flat and Nanopillared Surface

Koishi, T., Yasuoka, K. & Zeng, X. C., 2017 Oct 3, In : Langmuir. 33, 39, p. 10184-10192 9 p.

Research output: Contribution to journalArticle

Molecular dynamics
flat surfaces
molecular dynamics
Water
Computer simulation
12 Citations (Scopus)

Molecular dynamics simulations for resolving scaling laws of polyethylene melts

Takahashi, K. Z., Nishimura, R., Yasuoka, K. & Masubuchi, Y., 2017, In : Polymers. 9, 1, 24.

Research output: Contribution to journalArticle

Scaling laws
Polyethylene
Molecular dynamics
Polyethylenes
Computer simulation
6 Citations (Scopus)

Onset of static and dynamic universality among molecular models of polymers

Takahashi, K. Z., Nishimura, R., Yamato, N., Yasuoka, K. & Masubuchi, Y., 2017 Dec 1, In : Scientific Reports. 7, 1, 12379.

Research output: Contribution to journalArticle

polymer
timescale
prediction
simulation
power law
1 Citation (Scopus)

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

Tomobe, K., Yamamoto, E., Kojić, D., Sato, Y., Yasui, M. & Yasuoka, K., 2017 Dec 1, In : Science advances. 3, 12, e1701400.

Research output: Contribution to journalArticle

Water
Raman Spectrum Analysis
Monosaccharides
Molecular Dynamics Simulation
Hydrogen
2 Citations (Scopus)

Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

Doi, H. & Yasuoka, K., 2017 May 1, In : AIP Advances. 7, 5, 055018.

Research output: Contribution to journalArticle

replicas
simulation
lubrication
nanotechnology
slits

Seed concentration effect on heterogeneous nucleation by molecular dynamics

Suh, D. & Yasuoka, K., 2017 Jan 1, In : Interfacial Phenomena and Heat Transfer. 5, 3 Special issue, p. 223-229 7 p.

Research output: Contribution to journalArticle

Seed
Molecular dynamics
seeds
Nucleation
nucleation
8 Citations (Scopus)

Stability of excess electrons introduced by Ti interstitial in rutile TiO2(110) surface

Morita, K., Shibuya, T. & Yasuoka, K., 2017, In : Journal of Physical Chemistry C. 121, 3, p. 1602-1607 6 p.

Research output: Contribution to journalArticle

Titanium
rutile
interstitials
titanium
Electrons
7 Citations (Scopus)

Subsurface Polaron Concentration As a Factor in the Chemistry of Reduced TiO2 (110) Surfaces

Shibuya, T., Yasuoka, K., Mirbt, S. & Sanyal, B., 2017 Jun 1, In : Journal of Physical Chemistry C. 121, 21, p. 11325-11334 10 p.

Research output: Contribution to journalArticle

Gene Conversion
Polarons
polarons
chemistry
Oxygen vacancies
9 Citations (Scopus)
carbon nanotubes
Carbon Nanotubes
electric field
Electric fields
Pressure
3 Citations (Scopus)

Water permeation through the internal water pathway in activated GPCR rhodopsin

Tomobe, K., Yamamoto, E., Kholmurodov, K. & Yasuoka, K., 2017 May 1, In : PLoS One. 12, 5, e0176876.

Research output: Contribution to journalArticle

rhodopsin
Rhodopsin
Permeation
Water
Molecules
2016

1/f fluctuation and water permeation of aquaporins

Yamamoto, E. & Yasuoka, K., 2016 Apr 1, In : Kobunshi. 65, 4, p. 175-176 2 p.

Research output: Contribution to journalArticle

Aquaporins
Permeation
Water
Amino acids
Amino Acids
2 Citations (Scopus)

Aspect ratio effect of nanorods on heterogeneous nucleation rates by molecular dynamics

Suh, D. & Yasuoka, K., 2016, In : Journal of Thermal Science and Technology. 11, 3, p. 1-6 6 p.

Research output: Contribution to journalArticle

Nanorods
nanorods
Molecular dynamics
aspect ratio
Aspect ratio
16 Citations (Scopus)

Cage occupancy of methane hydrates from Gibbs ensemble Monte Carlo simulations

Brumby, P. E., Yuhara, D., Wu, D. T., Sum, A. K. & Yasuoka, K., 2016 Apr 15, In : Fluid Phase Equilibria. 413, p. 242-248 7 p.

Research output: Contribution to journalArticle

Methane
Hydrates
hydrates
methane
simulation
4 Citations (Scopus)

Condensation on nanorods by molecular dynamics

Suh, D. & Yasuoka, K., 2016 Jun 28, In : Journal of Chemical Physics. 144, 24, 244702.

Research output: Contribution to journalArticle

Nanorods
nanorods
Molecular dynamics
Condensation
condensation
2 Citations (Scopus)
mutations
hydration
proteins
simulation
molecular dynamics
23 Citations (Scopus)

Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics

Yamamoto, E., Kalli, A. C., Yasuoka, K. & Sansom, M. S. P., 2016 Aug 2, In : Structure. 24, 8, p. 1421-1431 11 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Phosphatidylinositol Phosphates
Membranes
Lipid Bilayers
Pleckstrin Homology Domains
15 Citations (Scopus)

Self-assembly behaviours of primitive and modern lipid membrane solutions: A coarse-grained molecular simulation study

Arai, N., Yoshimoto, Y., Yasuoka, K. & Ebisuzaki, T., 2016, In : Physical Chemistry Chemical Physics. 18, 28, p. 19426-19432 7 p.

Research output: Contribution to journalArticle

Membrane Lipids
Self assembly
lipids
self assembly
membranes
21 Citations (Scopus)

Self-Assembly of Janus Oligomers into Onion-like Vesicles with Layer-by-Layer Water Discharging Capability: A Minimalist Model

Arai, N., Yasuoka, K. & Zeng, X. C., 2016 Aug 23, In : ACS Nano. 10, 8, p. 8026-8037 12 p.

Research output: Contribution to journalArticle

Janus
Liposomes
oligomers
Oligomers
Self assembly
9 Citations (Scopus)

Separation of water-ethanol solutions with carbon nanotubes and electric fields

Winarto, Takaiwa, D., Yamamoto, E. & Yasuoka, K., 2016, In : Physical Chemistry Chemical Physics. 18, 48, p. 33310-33319 10 p.

Research output: Contribution to journalArticle

Carbon Nanotubes
ethyl alcohol
Ethanol
carbon nanotubes
Electric fields
4 Citations (Scopus)

Suppression of lattice thermal conductivity by mass-conserving cation mutation in multi-component semiconductors

Shibuya, T., Skelton, J. M., Jackson, A. J., Yasuoka, K., Togo, A., Tanaka, I. & Walsh, A., 2016 Oct 1, In : APL Materials. 4, 10, 104809.

Research output: Contribution to journalArticle

Lattice vibrations
Cations
Thermal conductivity
Positive ions
Semiconductor materials
2015
4 Citations (Scopus)

A determination of liquid-vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum

Takahashi, K. Z. & Yasuoka, K., 2015 Aug 13, In : Molecular Simulation. 41, 10-12, p. 795-800 6 p.

Research output: Contribution to journalArticle

Methanol
Linear Combination
methyl alcohol
Vapors
Liquid