• 4244 Citations
  • 37 h-Index
1994 …2020

Research output per year

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Research Output

2013

Water proton configurations in structures I, II, and H clathrate hydrate unit cells

Takeuchi, F., Hiratsuka, M., Ohmura, R., Alavi, S., Sum, A. K. & Yasuoka, K., 2013 Mar 28, In : Journal of Chemical Physics. 138, 12, 124504.

Research output: Contribution to journalArticle

78 Citations (Scopus)
2012

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)

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)

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)

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)

DS-CUDA: A middleware to use many GPUs in the cloud environment

Oikawa, M., Kawai, A., Nomura, K., Yasuoka, K., Yoshikawa, K. & Narumi, T., 2012 Dec 1, Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012. p. 1207-1214 8 p. 6495928. (Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012).

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

46 Citations (Scopus)

Estimation of breakdown electric-field strength while reflecting local structures of SiO 2 gate dielectrics using first-principles molecular orbital calculation technique

Seki, H., Shibuya, Y., Kobayashi, D., Nohira, H., Yasuoka, K. & Hirose, K., 2012 Apr 1, In : Japanese journal of applied physics. 51, 4 PART 2, 04DA07.

Research output: Contribution to journalArticle

1 Citation (Scopus)

GPU-accelerated computation of electron transfer

Höfinger, S., Acocella, A., Pop, S. C., Narumi, T., Yasuoka, K., Beu, T. & Zerbetto, F., 2012 Nov 5, In : Journal of Computational Chemistry. 33, 29, p. 2351-2356 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Kinetic analysis on nanoparticle condensation by molecular dynamics

Suh, D. & Yasuoka, K., 2012 Dec 1, ASME 2012 10th Int. Conf. on Nanochannels, Microchannels, and Minichannels Collocated with the ASME 2012 Heat Transfer Summer Conference and the ASME 2012 Fluids Engineering Division Sum, ICNMM 2012. p. 517-521 5 p. (ASME 2012 10th Int. Conf. on Nanochannels, Microchannels, and Minichannels Collocated with the ASME 2012 Heat Transfer Summer Conf. and the ASME 2012 Fluids Engineering Division Sum, ICNMM 2012).

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

8 Citations (Scopus)

MD simulations on the structure of onco-proteins P53: Wild-type and radioresistant mutant systems

Kholmurodov, K. T., Krasavin, E. A., Krylov, V. A., Dushanov, E. B., Korenkov, V. V., Yasuoka, K., Narumi, T., Ohno, Y., Taiji, M. & Ebisuzaki, T., 2012 Jan 1, Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc., p. 179-208 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Model of abnormal chromophore-protein interaction for E181K rhodopsin mutation: Computer molecular dynamics study

Feldman, T., Ostrovsky, M., Kholmurodov, K. & Yasuoka, K., 2012, In : Open Biochemistry Journal. 6, p. 102 1 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Molecular dynamics simulation of quasi-two-dimensional water clusters on ice nucleation protein

Murakami, D. & Yasuoka, K., 2012 Aug 7, In : Journal of Chemical Physics. 137, 5, 054303.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Molecular dynamics simulation of water adsorbed on ice nucleation protein

Murakami, D. & Yasuoka, K., 2012 Jan 1, Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc., p. 163-177 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular dynamics studies of the interaction between water and oxide surfaces

Dushanov, E., Kholmurodov, K. & Yasuoka, K., 2012 Nov 1, In : Physics of Particles and Nuclei Letters. 9, 6-7, p. 541-551 11 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Molecular dynamics study of ethanol solvated by water on the Pt (1 1 1) surface

Kholmurodov, K., Dushanov, E., Yasuoka, K., Khalil, H., Galal, A., Ahmed, S., Sweilam, N. & Moharram, H., 2012 Jun 19, In : Chemical Physics. 402, p. 41-47 7 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Molecular dynamics study on structual change in the surface membrane of an insonified coated microbubble

Ueki, F., Ito, S., Takahashi, K., Yasuoka, K. & Sugiura, T., 2012 Dec 1, 2012 IEEE International Ultrasonics Symposium, IUS 2012. p. 2282-2285 4 p. 6562339. (IEEE International Ultrasonics Symposium, IUS).

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

Molecular vibrations of methane molecules in the structure i clathrate hydrate from ab initio molecular dynamics simulation

Hiratsuka, M., Ohmura, R., Sum, A. K. & Yasuoka, K., 2012 Jan 28, In : Journal of Chemical Physics. 136, 4, 044508.

Research output: Contribution to journalArticle

35 Citations (Scopus)

Multibaric-multithermal ensemble study of liquid-solid phase transition in Lennard-Jones particles

Kaneko, T., Mitsutake, A. & Yasuoka, K., 2012 Sep, In : Journal of the Physical Society of Japan. 81, SUPPL. A, SA014.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Nanochannel with uniform and janus surfaces: Shear thinning and thickening in surfactant solution

Arai, N., Yasuoka, K. & Zeng, X. C., 2012 Feb 7, In : Langmuir. 28, 5, p. 2866-2872 7 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Nanoparticle growth analysis by molecular dynamics: Cubic seed

Suh, D. & Yasuoka, K., 2012 Dec 20, In : Journal of Physical Chemistry B. 116, 50, p. 14637-14649 13 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes

Höfinger, S., Yamamoto, E., Hirano, Y., Zerbetto, F., Narumi, T., Yasuoka, K. & Yasui, M., 2012 Sep 1, In : Biochimica et Biophysica Acta - Biomembranes. 1818, 9, p. 2234-2243 10 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Vibrational modes of methane in the structure H clathrate hydrate from ab initio molecular dynamics simulation

Hiratsuka, M., Ohmura, R., Sum, A. K. & Yasuoka, K., 2012 Oct 14, In : Journal of Chemical Physics. 137, 14, 144306.

Research output: Contribution to journalArticle

25 Citations (Scopus)
2011

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)

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)

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)

Cutoff radius effect of water configuration using the wolf method

Takahashi, K., Narumi, T. & Yasuoka, K., 2011, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. American Society of Mechanical Engineers, (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

Cutoff radius effect of water configuration using the wolf method

Takahashi, K., Narumi, T. & Yasuoka, K., 2011 Dec 1, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

Energy science of clathrate hydrates: Simulation-based advances

Sum, A. K., Wu, D. T. & Yasuoka, K., 2011 Mar, In : MRS Bulletin. 36, 3, p. 205-210 6 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Erratum: Thermodynamic properties of methanewater interface predicted by molecular dynamics simulations (Journal of Chemical Physics (2011) 134 (144702))

Sakamaki, R., Sum, A. K., Narumi, T., Ohmura, R. & Yasuoka, K., 2011 Dec 7, In : Journal of Chemical Physics. 135, 21, 219903.

Research output: Contribution to journalComment/debate

Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3

Narumi, T., Yasuoka, K., Taiji, M., Zerbetto, F. & Höfinger, S., 2011 Jul 1, In : Computer Journal. 54, 7, p. 1181-1187 7 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Fast quasi double-precision method with single-precision hardware to accelerate scientific applications

Narumi, T., Hamada, T., Nitadori, K., Sakamaki, R. & Yasuoka, K., 2011 Sep 1, In : International Journal of Computational Methods. 8, 3, p. 561-581 21 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Measurement of contact-angle hysteresis for droplets on nanopillared surface and in the Cassie and Wenzel states: A molecular dynamics simulation study

Koishi, T., Yasuoka, K., Fujikawa, S. & Zeng, X. C., 2011 Sep 27, In : ACS Nano. 5, 9, p. 6834-6842 9 p.

Research output: Contribution to journalArticle

98 Citations (Scopus)

Molecular dynamics simulation of quasi-two-dimensional water network on ice nucleation protein

Murakami, D. & Yasuoka, K., 2011, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. American Society of Mechanical Engineers, (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

Molecular dynamics simulation of three-dimensional heterogeneous nucleation

Suh, D. & Yasuoka, K., 2011 Dec 1, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

1 Citation (Scopus)

Molecular dynamics simulation of three-dimensional heterogeneous nucleation

Suh, D. & Yasuoka, K., 2011, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. American Society of Mechanical Engineers, (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

1 Citation (Scopus)

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

Sakamaki, R., Sum, A. K., Narumi, T. & Yasuoka, K., 2011 Mar 28, In : Journal of Chemical Physics. 134, 12, 124708.

Research output: Contribution to journalArticle

42 Citations (Scopus)

Multicanonical molecular dynamics simulation study of the liquid-solid and solid-solid transitions in Lennard-Jonse clusters

Kaneko, T., Yasuoka, K., Mitsutake, A. & Zeng, X. C., 2011 Dec 1, ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011. (ASME/JSME 2011 8th Thermal Engineering Joint Conference, AJTEC 2011).

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

Nanoparticle growth analysis by molecular dynamics: Spherical Seed

Suh, D. & Yasuoka, K., 2011 Sep 15, In : Journal of Physical Chemistry B. 115, 36, p. 10631-10645 15 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Non-Gaussian fluctuations resulting from power-law trapping in a lipid bilayer

Akimoto, T., Yamamoto, E., Yasuoka, K., Hirano, Y. & Yasui, M., 2011 Oct 20, In : Physical review letters. 107, 17, 178103.

Research output: Contribution to journalArticle

66 Citations (Scopus)

Size-dependent phase changes in water clusters

Kaneko, T., Akimoto, T., Yasuoka, K., Mitsutake, A. & Zeng, X. C., 2011 Oct 11, In : Journal of chemical theory and computation. 7, 10, p. 3083-3087 5 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Thermodynamic properties of methane/water interface predicted by molecular dynamics simulations

Sakamaki, R., Sum, A. K., Narumi, T., Ohmura, R. & Yasuoka, K., 2011 Apr 14, In : Journal of Chemical Physics. 134, 14, 144702.

Research output: Contribution to journalArticle

41 Citations (Scopus)
2010

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)

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)

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)

Erratum: Phases of hot nuclear matter at subnuclear densities (Physical Review C - Nuclear Physics (2004) 69 (055805))

Watanabe, G., Sato, K., Yasuoka, K. & Ebisuzaki, T., 2010 Apr 20, In : Physical Review C - Nuclear Physics. 81, 4, 049901.

Research output: Contribution to journalComment/debate

2 Citations (Scopus)

Erratum: Cell size dependence of orientational order of uniaxial liquid crystals in flat slit (Molecular Simulation (2008) 34:8 (761-773))

Mima, T., Narumi, T., Kameoka, S. & Yasuoka, K., 2010 Mar 1, In : Molecular Simulation. 36, 3, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Phase diagram of nuclear "pasta" and its uncertainties in supernova cores (Physical Review C - Nuclear Physics (2008) 77 (035806))

Sonoda, H., Watanabe, G., Sato, K., Yasuoka, K. & Ebisuzaki, T., 2010 Apr 20, In : Physical Review C - Nuclear Physics. 81, 4, 049902.

Research output: Contribution to journalComment/debate

10 Citations (Scopus)

Molecular dynamics simulations of urea-water binary droplets on flat and pillared hydrophobic surfaces

Koishi, T., Yasuoka, K., Zeng, X. C. & Fujikawa, S., 2010, In : Faraday Discussions. 146, p. 185-193 9 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Molecular mechanisms of how mercury inhibits water permeation through aquaporin-1: Understanding by molecular dynamics simulation

Hirano, Y., Okimoto, N., Kadohira, I., Suematsu, M., Yasuoka, K. & Yasui, M., 2010 Apr 21, In : Biophysical Journal. 98, 8, p. 1512-1519 8 p.

Research output: Contribution to journalArticle

59 Citations (Scopus)