All Stories

  1. Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations

    Article • Pure and Applied Chemistry, January 2014, De Gruyter

    Wataru Shinoda

  2. Free energy analysis along the stalk mechanism of membrane fusion

    Article • Soft Matter, January 2014, Royal Society of Chemistry

    Wataru Shinoda

  3. Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids

    Article • The Journal of Chemical Physics, November 2013, American Institute of Physics

    Wataru Shinoda

  4. A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation

    Article • The Journal of Chemical Physics, July 2013, American Institute of Physics

    Wataru Shinoda

  5. Intermolecular Interactions in Li+‐glyme and Li+‐glyme–TFSA− Complexes: Relationship with Physicochemical Properties of [Li(glyme)][TFSA] Ionic Liquids

    Article • ChemPhysChem, April 2013, Wiley

    Wataru Shinoda

  6. Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory

    Article • The Journal of Chemical Physics, March 2013, American Institute of Physics

    Wataru Shinoda

  7. Regioselective Recognition of a [60]Fullerene-Bisadduct by Cyclodextrin

    Article • The Journal of Organic Chemistry, February 2013, American Chemical Society (ACS)

    Wataru Shinoda

  8. Effect of different substituents on the water-solubility and stability properties of 1 : 2 [60]fullerene derivative·gamma-cyclodextrin complexes

    Article • Organic & Biomolecular Chemistry, January 2013, Royal Society of Chemistry

    Wataru Shinoda

  9. Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics

    Article • Soft Matter, January 2013, Royal Society of Chemistry

    Wataru Shinoda

  10. Computer Simulation of Self-Assembling Macromolecules

    Article • January 2013, Springer Science + Business Media

    Wataru Shinoda

  11. Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach

    Article • The Journal of Physical Chemistry C, October 2012, American Chemical Society (ACS)

    Wataru Shinoda

  12. Molecular Dynamics Study of Catanionic Bilayers Composed of Ion Pair Amphiphile with Double-Tailed Cationic Surfactant

    Article • Langmuir, May 2012, American Chemical Society (ACS)

    Wataru Shinoda

  13. Computer simulation studies of self-assembling macromolecules

    Article • Current Opinion in Structural Biology, April 2012, Elsevier

    Wataru Shinoda

  14. Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration

    Article • Chemical Physics Letters, January 2012, Elsevier

    Wataru Shinoda

  15. Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach

    Article • Soft Matter, January 2012, Royal Society of Chemistry

    Wataru Shinoda

  16. Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study

    Article • The Journal of Physical Chemistry B, December 2011, American Chemical Society (ACS)

    Wataru Shinoda

  17. Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics

    Article • Journal of Chemical Theory and Computation, November 2011, American Chemical Society (ACS)

    Wataru Shinoda

  18. Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems

    Article • The Journal of Chemical Physics, September 2011, American Institute of Physics

    Wataru Shinoda

  19. ChemInform Abstract: Molecular Dynamics Study of Isoprenoid‐Chained Lipids: Salient Features of Isoprenoid Chains as Compared with Ordinary Alkyl Chains

    Article • ChemInform, June 2011, Wiley

    Wataru Shinoda

  20. Development of a Coarse-Grained Model for the Surfactant Family of Linear Alkylbenzene Sulfonates

    Article • Biophysical Journal, February 2011, Elsevier

    Wataru Shinoda

  21. Effects of conformational flexibility of alkyl chains of cations on diffusion of ions in ionic liquids

    Article • Physical Chemistry Chemical Physics, January 2011, Royal Society of Chemistry

    Wataru Shinoda

  22. Free energy analysis of vesicle-to-bicelle transformation

    Article • Soft Matter, January 2011, Royal Society of Chemistry

    Wataru Shinoda

  23. 脂質膜・リポソームの分子シミュレーション

    Article • MEMBRANE, January 2011, The Membrane Society of Japan

    Wataru Shinoda

  24. Coarse-grained force field for ionic surfactants

    Article • Soft Matter, January 2011, Royal Society of Chemistry

    Wataru Shinoda

  25. Nanoscale carbon particles and the stability of lipid bilayers

    Article • Soft Matter, January 2011, Royal Society of Chemistry

    Wataru Shinoda

  26. Molecular dynamics study of nanoparticles and non-ionic surfactant at an oil–water interface

    Article • Soft Matter, January 2011, Royal Society of Chemistry

    Wataru Shinoda

  27. Molecular Dynamics Simulations of Nanoparticles and Surfactants at Oil/Water Interfaces

    Article • January 2011, American Chemical Society (ACS)

    Wataru Shinoda

  28. Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids

    Article • The Journal of Physical Chemistry B, November 2010, American Chemical Society (ACS)

    Wataru Shinoda

  29. Molecular Dynamics Study of Isoprenoid‐Chained Lipids: Salient Features of Isoprenoid Chains As Compared with Ordinary Alkyl Chains

    Article • October 2010, Wiley

    Wataru Shinoda

  30. Interactions of Perfluoroalkyltrifluoroborate Anions with Li Ion and Imidazolium Cation: Effects of Perfluoroalkyl Chain on Motion of Ions in Ionic Liquids

    Article • The Journal of Physical Chemistry B, August 2010, American Chemical Society (ACS)

    Wataru Shinoda

  31. Exploring the utility of coarse-grained water models for computational studies of interfacial systems

    Article • Molecular Physics, August 2010, Taylor & Francis

    Wataru Shinoda

  32. Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

    Article • The Journal of Physical Chemistry B, May 2010, American Chemical Society (ACS)

    Wataru Shinoda

  33. Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data

    Article • The Journal of Physical Chemistry B, April 2010, American Chemical Society (ACS)

    Wataru Shinoda

  34. Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes

    Article • The Journal of Physical Chemistry B, April 2010, American Chemical Society (ACS)

    Wataru Shinoda

  35. A mean field approach for computing solid-liquid surface tension for nanoscale interfaces

    Article • The Journal of Chemical Physics, February 2010, American Institute of Physics

    Wataru Shinoda

  36. Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

    Article • Chemical Physics Letters, February 2010, Elsevier

    Wataru Shinoda

  37. The shear hysteresis in lamellar structure of surfactant–water binary system

    Article • Chemical Physics, January 2010, Elsevier

    Wataru Shinoda

  38. 粗視化モデルによる両親媒性分子の自己組織化構造解析

    Article • Seibutsu Butsuri, January 2010, Biophysical Society of Japan

    Wataru Shinoda

  39. Size-dependent hydrophobic to hydrophilic transition for nanoparticles: A molecular dynamics study

    Article • The Journal of Chemical Physics, December 2009, American Institute of Physics

    Wataru Shinoda

  40. Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

    Article • Journal of Chemical Theory and Computation, July 2009, American Chemical Society (ACS)

    Wataru Shinoda

  41. Molecular Dynamics Simulations of Ionic Liquids: Cation and Anion Dependence of Self-Diffusion Coefficients of Ions

    Article • The Journal of Physical Chemistry B, July 2009, American Chemical Society (ACS)

    Wataru Shinoda

  42. Models for Phosphatidylglycerol Lipids Put to a Structural Test

    Article • The Journal of Physical Chemistry B, April 2009, American Chemical Society (ACS)

    Wataru Shinoda

  43. Computational exploration of novel silicon nanostructures

    Article • March 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Wataru Shinoda

  44. Area per Ligand as a Function of Nanoparticle Radius: A Theoretical and Computer Simulation Approach

    Article • Langmuir, January 2009, American Chemical Society (ACS)

    Wataru Shinoda

  45. Fluorination effects on structure and dynamics of phospholipid bilayer: A molecular dynamics study

    Article • Chemical Physics Letters, January 2009, Elsevier

    Wataru Shinoda

  46. Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models

    Article • September 2008, Taylor & Francis

    Wataru Shinoda

  47. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study

    Article • The Journal of Physical Chemistry B, August 2008, American Chemical Society (ACS)

    Wataru Shinoda

  48. Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods

    Article • Journal of Mathematical Chemistry, June 2008, Springer Science + Business Media

    Wataru Shinoda

  49. Efficient free energy calculation of water across lipid membranes

    Article • Journal of Computational Chemistry, June 2008, Wiley

    Wataru Shinoda

  50. Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation

    Article • The Journal of Chemical Physics, May 2008, American Institute of Physics

    Wataru Shinoda

  51. United-Atom Acyl Chains for CHARMM Phospholipids

    Article • The Journal of Physical Chemistry B, May 2008, American Chemical Society (ACS)

    Wataru Shinoda

  52. Electronic and optical properties of polyicosahedral Si nanostructures: A first-principles study

    Article • Physical Review B, February 2008, American Physical Society (APS)

    Wataru Shinoda

  53. Coarse-grained molecular modeling of non-ionic surfactant self-assembly

    Article • Soft Matter, January 2008, Royal Society of Chemistry

    Wataru Shinoda

  54. Molecular dynamics simulation of an archaeal lipid bilayer with sodium chloride

    Article • Physical Chemistry Chemical Physics, January 2007, Royal Society of Chemistry

    Wataru Shinoda

  55. Molecular dynamics simulations of self-organized polyicosahedral Si nanowire

    Article • The Journal of Chemical Physics, August 2006, American Institute of Physics

    Wataru Shinoda

  56. Molecular dynamics simulation of icosahedral Si quantum dot formation from liquid droplets

    Article • Physical Review B, December 2005, American Physical Society (APS)

    Wataru Shinoda

  57. Molecular Dynamics Study of Bipolar Tetraether Lipid Membranes

    Article • Biophysical Journal, November 2005, Elsevier

    Wataru Shinoda

  58. Intermolecular interaction between the pendant chain of perfluorinated ionomer and methanol

    Article • Journal of Fluorine Chemistry, October 2005, Elsevier

    Wataru Shinoda

  59. Calculation of heat capacities of light and heavy water by path-integral molecular dynamics

    Article • The Journal of Chemical Physics, September 2005, American Institute of Physics

    Wataru Shinoda

  60. Molecular Dynamics Study of the Methanol Effect on the Membrane Morphology of Perfluorosulfonic Ionomers

    Article • The Journal of Physical Chemistry B, August 2005, American Chemical Society (ACS)

    Wataru Shinoda

  61. Quantum simulation of the heat capacity of water

    Article • Physical Review E, April 2005, American Physical Society (APS)

    Wataru Shinoda

  62. Spatial confinement effect on the atomic structure of solid argon

    Article • The Journal of Chemical Physics, March 2005, American Institute of Physics

    Wataru Shinoda

  63. Molecular Dynamics Simulation of Swollen Membrane of Perfluorinated Ionomer

    Article • The Journal of Physical Chemistry B, February 2005, American Chemical Society (ACS)

    Wataru Shinoda

  64. Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers

    Article • The Journal of Chemical Physics, November 2004, American Institute of Physics

    Wataru Shinoda

  65. Can such Long Time Steps Really be used in Dissipative Particle Dynamics Simulations?

    Article • Molecular Simulation, November 2004, Taylor & Francis

    Wataru Shinoda

  66. Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study

    Article • Physical Review B, August 2004, American Physical Society (APS)

    Wataru Shinoda

  67. Two-dimensional self-assembled structures of adenine molecules: modeling and simulation

    Article • Surface Science, May 2004, Elsevier

    Wataru Shinoda

  68. Dynamics of a highly branched lipid bilayer: a molecular dynamics study

    Article • Chemical Physics Letters, May 2004, Elsevier

    Wataru Shinoda

  69. Rapid estimation of elastic constants by molecular dynamics simulation under constant stress

    Article • Physical Review B, April 2004, American Physical Society (APS)

    Wataru Shinoda

  70. Intermolecular interaction between the pendant chain of perfluorinated ionomer and water

    Article • Physical Chemistry Chemical Physics, January 2004, Royal Society of Chemistry

    Wataru Shinoda

  71. 計算機科学から生体膜研究へのアプローチ 脂質膜の構造安定性と透過性の分子動力学シミュレーションによる予測

    Article • MEMBRANE, January 2004, The Membrane Society of Japan

    Wataru Shinoda

  72. Molecular Dynamics Study on the Effect of Chain Branching on the Physical Properties of Lipid Bilayers:  Structural Stability

    Article • The Journal of Physical Chemistry B, November 2003, American Chemical Society (ACS)

    Wataru Shinoda

  73. Rigid‐body dynamics in the isothermal‐isobaric ensemble: A test on the accuracy and computational efficiency

    Article • Journal of Computational Chemistry, April 2003, Wiley

    Wataru Shinoda

  74. Self-guided molecular dynamics in the isothermal–isobaric ensemble

    Article • Chemical Physics Letters, February 2001, Elsevier

    Wataru Shinoda

  75. Molecular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: an effect of the potential force fields on the membrane structure

    Article • Journal of Molecular Liquids, February 2001, Elsevier

    Wataru Shinoda

  76. Parallel molecular dynamics simulation: Implementation of PVM for a lipid membrane

    Article • Computer Physics Communications, February 1999, Elsevier

    Wataru Shinoda

  77. Molecular Dynamics Study on Electrostatic Properties of a Lipid Bilayer:  Polarization, Electrostatic Potential, and the Effects on Structure and Dynamics of Water near the Interface

    Article • The Journal of Physical Chemistry B, August 1998, American Chemical Society (ACS)

    Wataru Shinoda

  78. A Voronoi analysis of lipid area fluctuation in a bilayer

    Article • The Journal of Chemical Physics, July 1998, American Institute of Physics

    Wataru Shinoda

  79. Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics

    Article • The Journal of Chemical Physics, April 1997, American Institute of Physics

    Wataru Shinoda

  80. Molecular dynamics simulation of the dipalmitoylphosphatidylcholine (DPPC) lipid bilayer in the fluid phase using the Nosé-Parrinello-Rahman NPT ensemble

    Article • Chemical Physics Letters, January 1995, Elsevier

    Wataru Shinoda