• 4244 Citations
  • 37 h-Index
1994 …2020

Research output per year

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Research Output

Article

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

15 Citations (Scopus)

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

Accelerating molecular dynamics simulations on playstation 3 platform using virtual-grape programming model

Narumi, T., Kameoka, S., Taiji, M. & Yasuoka, K., 2008, In : SIAM Journal on Scientific Computing. 30, 6, p. 3108-3125 18 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Accelerating molecular dynamics simulation using graphics processing unit

Myung, H. J., Sakamaki, R., Oh, K. J., Narumi, T., Yasuoka, K. & Lee, S., 2010 Dec 20, In : Bulletin of the Korean Chemical Society. 31, 12, p. 3639-3643 5 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

Takahashi, K., Narumi, T. & Yasuoka, K., 2011 Nov 7, In : Journal of Chemical Physics. 135, 17, 174108.

Research output: Contribution to journalArticle

17 Citations (Scopus)

Activation energy calculations for formamide-TiO2 and formamide-pt interactions in the presence of water

Dushanov, E., Kholmurodov, K. & Yasuoka, K., 2013 Apr 17, In : Open Biochemistry Journal. 7, 1, p. 33-43 11 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

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

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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)

A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates

Hiratsuka, M., Ohmura, R., Sum, A. K., Alavi, S. & Yasuoka, K., 2015 May 21, In : Physical Chemistry Chemical Physics. 17, 19, p. 12639-12647 9 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Analysis of crystal growth of methane hydrate using molecular dynamics simulation

Yuhara, D., Hiratsuka, M., Takaiwa, D. & Yasuoka, K., 2015 Aug 13, In : Molecular Simulation. 41, 10-12, p. 918-922 5 p.

Research output: Contribution to journalArticle

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

3 Citations (Scopus)

An analysis of natural convection using the thermal finite element discrete Boltzmann equation

Seino, M., Tanahashi, T. & Yasuoka, K., 2011 Jan 1, In : Computers and Fluids. 40, 1, p. 113-117 5 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

An improved isotropic periodic sum method that uses linear combinations of basis potentials

Takahashi, K. Z., Narumi, T., Suh, D. & Yasuoka, K., 2012 Nov 13, In : Journal of chemical theory and computation. 8, 11, p. 4503-4516 14 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Anisotropic molecular clustering in liquid ethanol induced by a charged fully hydroxylated silicon dioxide (SiO2) surface

Andoh, Y., Kurahashi, K., Sakuma, H., Yasuoka, K. & Kurihara, K., 2007 Nov 14, In : Chemical Physics Letters. 448, 4-6, p. 253-257 5 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

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)

Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface

Yamamoto, E., Kalli, A. C., Akimoto, T., Yasuoka, K. & Sansom, M. S. P., 2015 Dec 14, In : Scientific reports. 5, 18245.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Application of isotropic periodic sum method for 4-pentyl-4′-cyanobiphenyl liquid crystal

Nozawa, T., Takahashi, K., Kameoka, S., Narumi, T. & Yasuoka, K., 2015 Aug 13, In : Molecular Simulation. 41, 10-12, p. 927-935 9 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Approaches for Controlling the Temperature and Pressure Range in Generalized NPT Ensembles

Doi, H. & Yasuoka, K., 2015 Sep 8, In : Journal of Chemical Theory and Computation. 11, 9, p. 4370-4376 7 p.

Research output: Contribution to journalArticle

A Smooth-Particle Mesh Ewald Method for DL_POLY Molecular Dynamics Simulation Package on the Fujitsu VPP700

Kholmurodov, K., Smith, W., Yasuoka, K., Darden, T. & Ebisuzaki, T., 2000 Jan 1, In : Journal of Computational Chemistry. 21, 13, p. 1187-1191 5 p.

Research output: Contribution to journalArticle

41 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

2 Citations (Scopus)

Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel

Arai, N., Yasuoka, K., Koishi, T. & Ebisuzaki, T., 2010 Oct 26, In : ACS Nano. 4, 10, p. 5905-5913 9 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

A systematic study of polarons due to oxygen vacancy formation at the rutile TiO 2(110) surface by GGA+U and HSE06 methods

Shibuya, T., Yasuoka, K., Mirbt, S. & Sanyal, B., 2012 Oct 31, In : Journal of Physics Condensed Matter. 24, 43, 435504.

Research output: Contribution to journalArticle

50 Citations (Scopus)

A vesicle cell under collision with a Janus or homogeneous nanoparticle: Translocation dynamics and late-stage morphology

Arai, N., Yasuoka, K. & Zeng, X. C., 2013 Oct 7, In : Nanoscale. 5, 19, p. 9089-9100 12 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

Bipolaron formation induced by oxygen vacancy at rutile TiO 2(110) surfaces

Shibuya, T., Yasuoka, K., Mirbt, S. & Sanyal, B., 2014 May 8, In : Journal of Physical Chemistry C. 118, 18, p. 9429-9435 7 p.

Research output: Contribution to journalArticle

19 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)

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)

Cell size dependence of orientational order of uniaxial liquid crystals in flat slit

Mima, T., Narumi, T., Kameoka, S. & Yasuoka, K., 2008 Jul 1, In : Molecular Simulation. 34, 8, p. 761-773 13 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface

Koishi, T., Yasuoka, K., Fujikawa, S., Ebisuzaki, T. & Xiao, C. Z., 2009 May 26, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 21, p. 8435-8440 6 p.

Research output: Contribution to journalArticle

296 Citations (Scopus)

Common force field thermodynamics of cholesterol

Giangreco, F., Yamamoto, E., Hirano, Y., Hodoscek, M., Knecht, V., Di Giosia, M., Calvaresi, M., Zerbetto, F., Yasuoka, K., Narumi, T., Yasui, M. & Höfinger, S., 2013, In : The Scientific World Journal. 2013, 207287.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system

Nozawa, T., Takahashi, K. Z., Narumi, T. & Yasuoka, K., 2015 Dec 15, In : Journal of Computational Chemistry. 36, 32, p. 2406-2411 6 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Computer simulation of fluid phase change: Vapor nucleation and bubble formation dynamics

Kinjo, T., Ohguchi, K., Yasuoka, K. & Matsumoto, M., 1999 Feb, In : Computational Materials Science. 14, 1-4, p. 138-141 4 p.

Research output: Contribution to journalArticle

28 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)

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)

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)

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

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced poisson boltzmann approach

Narumi, T., Yasuoka, K., Taiji, M. & Höfinger, S., 2009 Nov 15, In : Journal of Computational Chemistry. 30, 14, p. 2351-2357 7 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid

Takahashi, K., Yasuoka, K. & Narumi, T., 2007 Sep 28, In : Journal of Chemical Physics. 127, 11, 114511.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid-vapor interfaces of water

Takahashi, K., Narumi, T. & Yasuoka, K., 2011 May 7, In : Journal of Chemical Physics. 134, 17, 174112.

Research output: Contribution to journalArticle

37 Citations (Scopus)

Cut-off radius effect of the isotropic periodic sum method for polar molecules in a bulk water system

Takahashi, K., Narumi, T. & Yasuoka, K., 2012 Apr 1, In : Molecular Simulation. 38, 5, p. 397-403 7 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Cutoff radius effect of the isotropic periodic sum method in homogeneous system. II. Water

Takahashi, K., Narumi, T. & Yasuoka, K., 2010 Jul 7, In : Journal of Chemical Physics. 133, 1, 014109.

Research output: Contribution to journalArticle

29 Citations (Scopus)

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

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

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)

Diffusive nature of xenon anesthetic changes properties of a lipid bilayer: Molecular dynamics simulations

Yamamoto, E., Akimoto, T., Shimizu, H., Hirano, Y., Yasui, M. & Yasuoka, K., 2012 Aug 2, In : Journal of Physical Chemistry B. 116, 30, p. 8989-8995 7 p.

Research output: Contribution to journalArticle

43 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)

Dynamic interactions of cations, water and lipids and influence on membrane fluidity

Kagawa, R., Hirano, Y., Taiji, M., Yasuoka, K. & Yasui, M., 2013 May 5, In : Journal of Membrane Science. 435, p. 130-136 7 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Dynamics near a liquid surface: Mechanisms of evaporation and condensation

Yasuoka, K., Matsumoto, M. & Kataoka, Y., 1995 Nov, In : Journal of Molecular Liquids. 65-66, C, p. 329-332 4 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)