• 4244 Citations
  • 37 h-Index
1994 …2020

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2020

A biointerface effect on the self-assembly of ribonucleic acids: A possible mechanism of RNA polymerisation in the self-replication cycle

Arai, N., Kobayashi, Y. & Yasuoka, K., 2020 Mar 28, In : Nanoscale. 12, 12, p. 6691-6698 8 p.

Research output: Contribution to journalArticle

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

Pua, K., Yuhara, D., Ayuba, S. & Yasuoka, K., 2020 Apr, In : PloS one. 15, 4, e0231714.

Research output: Contribution to journalArticle

Open Access

Mechanism for H2diffusion in sII hydrates by molecular dynamics simulations

Hasegawa, T., Brumby, P. E., Yasuoka, K. & Sum, A. K., 2020 Aug 7, In : Journal of Chemical Physics. 153, 5, 054706.

Research output: Contribution to journalArticle

Open Access

The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study

Anggayasti, W. L., Ogino, K., Yamamoto, E., Helmerhorst, E., Yasuoka, K. & Mancera, R. L., 2020, In : Computational and Structural Biotechnology Journal. 18, p. 1160-1172 13 p.

Research output: Contribution to journalArticle

Open Access
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

2 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

3 Citations (Scopus)

Crystal Engineering of Bi2WO6 to Polar Aurivillius-Phase Oxyhalides

Morita, K., Park, J. S., Kim, S., Yasuoka, K. & Walsh, A., 2019 Dec 5, In : Journal of Physical Chemistry C. 123, 48, p. 29155-29161 7 p.

Research output: Contribution to journalArticle

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

1 Citation (Scopus)

Method to implement interaction surfaces with virtual companion particles for molecular dynamics simulations

Koishi, T., Yasuoka, K. & Zeng, X. C., 2019 Sep 12, In : Journal of Chemical and Engineering Data. 64, 9, p. 3693-3700 8 p.

Research output: Contribution to journalArticle

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

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

2018

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

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

Research output: Contribution to journalArticle

2 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

3 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

2 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

8 Citations (Scopus)

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

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

1 Citation (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

7 Citations (Scopus)

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

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

19 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

6 Citations (Scopus)

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

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

1 Citation (Scopus)

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

2 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

9 Citations (Scopus)
2017

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, In : Molecular Simulation. 43, 13-16, p. 1196-1201 6 p.

Research output: Contribution to journalArticle

5 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

12 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, In : Science Advances. 3, 1, e1601871.

Research output: Contribution to journalArticle

24 Citations (Scopus)
3 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

25 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

2 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

10 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

15 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

10 Citations (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, In : Science Advances. 3, 12, e1701400.

Research output: Contribution to journalArticle

3 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

2 Citations (Scopus)

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

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

12 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

7 Citations (Scopus)
11 Citations (Scopus)

Water permeation through the internal water pathway in activated GPCR rhodopsin

Tomobe, K., Yamamoto, E., Kholmurodov, K. & Yasuoka, K., 2017 May, In : PloS one. 12, 5, e0176876.

Research output: Contribution to journalArticle

6 Citations (Scopus)
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

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

2 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

20 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

4 Citations (Scopus)
2 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

34 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

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

26 Citations (Scopus)

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

Winarto, Takaiwa, D., Yamamoto, E. & Yasuoka, K., 2016 Jan 1, In : Physical Chemistry Chemical Physics. 18, 48, p. 33310-33319 10 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)