All Stories

  1. pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Wataru Shinoda

  2. Hydrophobicity-Governed Protein Adsorption on Poly(ω-methoxyalkyl acrylate) Surfaces: A Coarse-Grained Molecular Dynamics Study

    Article • Journal of Chemical Theory and Computation, September 2025, American Chemical Society (ACS)

    Wataru Shinoda

  3. SPICA Force Field for Nucleic Acids and Its Application to Lipid Nanoparticles

    Article • The Journal of Physical Chemistry B, June 2025, American Chemical Society (ACS)

    Wataru Shinoda

  4. In Silico Study of Ionizable Lipid Nanoparticles Using the SPICA Force Field

    Article • Journal of Chemical Theory and Computation, June 2025, American Chemical Society (ACS)

    Wataru Shinoda

  5. Asymmetry and heterogeneity in the plasma membrane

    Article • Biophysical Journal, June 2025, Elsevier

    Wataru Shinoda

  6. Unraveling the Molecular Mechanism of Transient Multilamellar Formation in Ethanol-Modified Vesicle Solutions

    Article • Langmuir, May 2025, American Chemical Society (ACS)

    Wataru Shinoda

  7. Asymmetry and Heterogeneity in the Plasma Membrane

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Wataru Shinoda

  8. Discrepant lithium transference numbers due to heterogeneous speciation

    Article • Physical Chemistry Chemical Physics, January 2025, Royal Society of Chemistry

    Frederik Philippi, Wataru Shinoda

  9. Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation

    Article • Nanoscale, January 2025, Royal Society of Chemistry

    Wataru Shinoda

  10. NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using 13C and 19F labelling

    Article • Organic & Biomolecular Chemistry, January 2025, Royal Society of Chemistry

    Wataru Shinoda

  11. Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA

    Article • Lab on a Chip, January 2025, Royal Society of Chemistry

    Wataru Shinoda

  12. Linear ether-based highly concentrated electrolytes for Li–sulfur batteries

    Article • Faraday Discussions, January 2024, Royal Society of Chemistry

    Wataru Shinoda

  13. Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations

    Article • Nanoscale Advances, January 2024, Royal Society of Chemistry

    Wataru Shinoda

  14. pSPICA Force Field Extended for Proteins and Peptides

    Article • Journal of Chemical Information and Modeling, December 2023, American Chemical Society (ACS)

    Wataru Shinoda

  15. Molecular Level Origin of Ion Dynamics in Highly Concentrated Electrolytes

    Article • The Journal of Physical Chemistry B, November 2023, American Chemical Society (ACS)

    Wataru Shinoda, Frederik Philippi

  16. Improved Protein Model in SPICA Force Field

    Article • Journal of Chemical Theory and Computation, November 2023, American Chemical Society (ACS)

    Wataru Shinoda

  17. HER‐2‐Targeted Boron Neutron Capture Therapy with Carborane‐integrated Immunoliposomes Prepared via an Exchanging Reaction

    Article • Chemistry - A European Journal, November 2023, Wiley

    Wataru Shinoda

  18. Pragmatic Coarse-Graining of Proteins: Models and Applications

    Article • Journal of Chemical Theory and Computation, October 2023, American Chemical Society (ACS)

    Wataru Shinoda

  19. Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy

    Article • Biosensors and Bioelectronics, August 2023, Elsevier

    Wataru Shinoda

  20. Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion

    Article • The Journal of Physical Chemistry B, July 2023, American Chemical Society (ACS)

    Wataru Shinoda

  21. Complex Energy Landscapes of Self-Assembled Vesicles

    Article • Journal of the American Chemical Society, July 2023, American Chemical Society (ACS)

    Wataru Shinoda

  22. Lithium-Ion Dynamics in Sulfolane-Based Highly Concentrated Electrolytes

    Article • The Journal of Physical Chemistry C, July 2023, American Chemical Society (ACS)

    Wataru Shinoda

  23. Li-Ion Transport and Solution Structure in Sulfolane-Based Localized High-Concentration Electrolytes

    Article • The Journal of Physical Chemistry C, June 2023, American Chemical Society (ACS)

    Wataru Shinoda

  24. Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes

    Article • Journal of the American Chemical Society, February 2023, American Chemical Society (ACS)

    Wataru Shinoda

  25. Fluorescence Turn‐on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa Cells, andE. coli

    Article • Chemistry - A European Journal, January 2023, Wiley

    Wataru Shinoda

  26. Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, September 2022, Elsevier

    Wataru Shinoda

  27. Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study

    Article • Science Advances, June 2022, American Association for the Advancement of Science

    Wataru Shinoda

  28. SPICA Force Field for Proteins and Peptides

    Article • Journal of Chemical Theory and Computation, April 2022, American Chemical Society (ACS)

    Wataru Shinoda

  29. Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study

    Article • Physical Chemistry Chemical Physics, January 2022, Royal Society of Chemistry

    Wataru Shinoda

  30. All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution

    Article • The Journal of Chemical Physics, October 2021, American Institute of Physics

    Wataru Shinoda

  31. Domain Formation in Charged Polymer Vesicles

    Article • Macromolecules, October 2021, American Chemical Society (ACS)

    Wataru Shinoda

  32. Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations

    Article • The Journal of Physical Chemistry B, May 2021, American Chemical Society (ACS)

    Wataru Shinoda

  33. Hemimicelle formation of semi-fluorocarbon chains at air–water interface: coarse-grained molecular dynamics study with an extension of the SPICA force field

    Article • Molecular Physics, April 2021, Taylor & Francis

    Wataru Shinoda

  34. Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

    Article • Proceedings of the National Academy of Sciences, March 2021, Proceedings of the National Academy of Sciences

    Wataru Shinoda

  35. Chain-End Modification: A Starting Point for Controlling Polymer Crystal Nucleation

    Article • Macromolecules, February 2021, American Chemical Society (ACS)

    Wataru Shinoda

  36. Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: plausible reaction path during discharge of lithium–sulfur battery

    Article • Physical Chemistry Chemical Physics, January 2021, Royal Society of Chemistry

    Wataru Shinoda

  37. Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

    Article • Journal of Chemical Theory and Computation, November 2020, American Chemical Society (ACS)

    Wataru Shinoda

  38. Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Wataru Shinoda

  39. Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine

    Article • Biochemistry, September 2020, American Chemical Society (ACS)

    Wataru Shinoda

  40. Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation

    Article • The Journal of Chemical Physics, June 2020, American Institute of Physics

    Wataru Shinoda

  41. Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations

    Article • The Journal of Physical Chemistry Letters, June 2020, American Chemical Society (ACS)

    Wataru Shinoda

  42. Effect of the Packing Density on the Surface Hydrophobicity of ω-Functionalized (−CF3, −CH3, −OCH3, and −OH) Self-Assembled Monolayers: A Molecular Dynamics Study

    Article • The Journal of Physical Chemistry C, May 2020, American Chemical Society (ACS)

    Wataru Shinoda

  43. Property Decoupling across the Embryonic Nucleus–Melt Interface during Polymer Crystal Nucleation

    Article • The Journal of Physical Chemistry B, May 2020, American Chemical Society (ACS)

    Wataru Shinoda

  44. Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene

    Article • Polymers, February 2020, MDPI AG

    Wataru Shinoda

  45. Molecular simulation of the shape deformation of a polymersome

    Article • Soft Matter, January 2020, Royal Society of Chemistry

    Wataru Shinoda

  46. The Amphotericin B–Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly

    Article • Biochemistry, December 2019, American Chemical Society (ACS)

    Wataru Shinoda

  47. Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein

    Article • Journal of Chemical Information and Modeling, November 2019, American Chemical Society (ACS)

    Wataru Shinoda

  48. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model

    Article • Journal of Chemical Theory and Computation, November 2019, American Chemical Society (ACS)

    Wataru Shinoda

  49. Divining the shape of nascent polymer crystal nuclei

    Article • The Journal of Chemical Physics, October 2019, American Institute of Physics

    Wataru Shinoda

  50. Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study

    Article • Langmuir, October 2019, American Chemical Society (ACS)

    Wataru Shinoda

  51. Large-scale molecular dynamics simulation of perfluorosulfonic acid membranes: Remapping coarse-grained to all-atomistic simulations

    Article • Polymer, October 2019, Elsevier

    Wataru Shinoda

  52. All-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC

    Article • Polymer, September 2019, Elsevier

    Wataru Shinoda

  53. Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes

    Article • Biochemistry, August 2019, American Chemical Society (ACS)

    Wataru Shinoda

  54. tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules

    Article • Journal of Chemical Information and Modeling, August 2019, American Chemical Society (ACS)

    Wataru Shinoda

  55. Hydrogen Permeation in Hydrated Perfluorosulfonic Acid Polymer Membranes: Effect of Polymer Crystallinity and Equivalent Weight

    Article • The Journal of Physical Chemistry C, August 2019, American Chemical Society (ACS)

    Wataru Shinoda

  56. Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation

    Article • Langmuir, July 2019, American Chemical Society (ACS)

    Wataru Shinoda

  57. Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup

    Article • Biophysical Journal, July 2019, Elsevier

    Wataru Shinoda

  58. A coarse-grain model for entangled polyethylene melts and polyethylene crystallization

    Article • The Journal of Chemical Physics, June 2019, American Institute of Physics

    Wataru Shinoda

  59. Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ′), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied by X-ray Diffraction and Molecular Dynamics Simulation

    Article • Langmuir, June 2019, American Chemical Society (ACS)

    Wataru Shinoda

  60. Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model

    Article • Polymer, April 2019, Elsevier

    Wataru Shinoda

  61. SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol

    Article • Journal of Chemical Theory and Computation, December 2018, American Chemical Society (ACS)

    Wataru Shinoda

  62. Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes

    Article • The Journal of Physical Chemistry B, November 2018, American Chemical Society (ACS)

    Wataru Shinoda

  63. Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction

    Article • Chemical Physics Letters, August 2018, Elsevier

    Wataru Shinoda

  64. Exploring the effect of pendent side chain length on the structural and mechanical properties of hydrated perfluorosulfonic acid polymer membranes by molecular dynamics simulation

    Article • Polymer, June 2018, Elsevier

    Wataru Shinoda

  65. Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

    Article • The Journal of Chemical Physics, January 2018, American Institute of Physics

    Wataru Shinoda

  66. Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals

    Article • Journal of Chemical Information and Modeling, January 2018, American Chemical Society (ACS)

    Wataru Shinoda

  67. Polymer Electrolytes Containing Solvate Ionic Liquids: A New Approach To Achieve High Ionic Conductivity, Thermal Stability, and a Wide Potential Window

    Article • Chemistry of Materials, December 2017, American Chemical Society (ACS)

    Wataru Shinoda

  68. Molecular Dynamics Study on the Mechanical Deformation of Hydrated Perfluorosulfonic Acid Polymer Membranes

    Article • The Journal of Physical Chemistry C, September 2017, American Chemical Society (ACS)

    Wataru Shinoda

  69. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

    Article • The Journal of Chemical Physics, September 2017, American Institute of Physics

    Wataru Shinoda

  70. Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission

    Article • Proceedings of the National Academy of Sciences, August 2017, Proceedings of the National Academy of Sciences

    Wataru Shinoda

  71. Effect of the cation on the stability of cation–glyme complexes and their interactions with the [TFSA]− anion

    Article • Physical Chemistry Chemical Physics, January 2017, Royal Society of Chemistry

    Wataru Shinoda

  72. Molecular Dynamics Study of the Morphology of Hydrated Perfluorosulfonic Acid Polymer Membranes

    Article • The Journal of Physical Chemistry C, November 2016, American Chemical Society (ACS)

    Wataru Shinoda

  73. Permeability across lipid membranes

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, October 2016, Elsevier

    Wataru Shinoda

  74. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    Article • The Journal of Chemical Physics, December 2015, American Institute of Physics

    Wataru Shinoda

  75. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism

    Article • The Journal of Chemical Physics, October 2015, American Institute of Physics

    Wataru Shinoda

  76. Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS

    Article • Computer Physics Communications, May 2015, Elsevier

    Wataru Shinoda

  77. Structures of [Li(glyme)]+ complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Wataru Shinoda

  78. [70]Fullerenes Assist the Formation of Phospholipid Bicelles at Low Lipid Concentrations

    Article • Langmuir, October 2014, American Chemical Society (ACS)

    Wataru Shinoda

  79. Thermodynamic Stability of [60]Fullerene and γ-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation

    Article • The Journal of Physical Chemistry C, May 2014, American Chemical Society (ACS)

    Wataru Shinoda

  80. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  82. 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, Wataru Shinoda

  83. 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, Wataru Shinoda

  84. 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, Wataru Shinoda

  85. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  87. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  89. 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, Wataru Shinoda

  90. 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, Wataru Shinoda

  91. Computer simulation studies of self-assembling macromolecules

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

    Wataru Shinoda, Wataru Shinoda

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

    Article • Chemical Physics Letters, January 2012, Elsevier

    Wataru Shinoda, Wataru Shinoda

  93. 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, Wataru Shinoda

  94. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  96. 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, Wataru Shinoda

  97. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  99. Coarse-grained force field for ionic surfactants

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

    Wataru Shinoda, Wataru Shinoda

  100. Nanoscale carbon particles and the stability of lipid bilayers

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

    Wataru Shinoda, Wataru Shinoda

  101. 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, Wataru Shinoda

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

    Article • January 2011, American Chemical Society (ACS)

    Wataru Shinoda, Wataru Shinoda

  103. 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, Wataru Shinoda

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

    Article • October 2010, Wiley

    Wataru Shinoda, Wataru Shinoda

  105. 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, Wataru Shinoda

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

    Article • Molecular Physics, August 2010, Taylor & Francis

    Wataru Shinoda, Wataru Shinoda

  107. 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, Wataru Shinoda

  108. 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, Wataru Shinoda

  109. 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, Wataru Shinoda

  110. 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, Wataru Shinoda

  111. 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, Wataru Shinoda

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

    Article • Chemical Physics, January 2010, Elsevier

    Wataru Shinoda, Wataru Shinoda

  113. 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, Wataru Shinoda

  114. Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

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

    Wataru Shinoda, Wataru Shinoda

  115. 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, Wataru Shinoda

  116. Models for Phosphatidylglycerol Lipids Put to a Structural Test

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

    Wataru Shinoda, Wataru Shinoda

  117. Computational exploration of novel silicon nanostructures

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

    Wataru Shinoda, Wataru Shinoda

  118. 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, Wataru Shinoda

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

    Article • Chemical Physics Letters, January 2009, Elsevier

    Wataru Shinoda, Wataru Shinoda

  120. 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, Wataru Shinoda

  121. Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

    Article • Science, August 2008, American Association for the Advancement of Science

    Wataru Shinoda

  122. 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, Wataru Shinoda

  123. Efficient free energy calculation of water across lipid membranes

    Article • Journal of Computational Chemistry, June 2008, Wiley

    Wataru Shinoda, Wataru Shinoda

  124. 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, Wataru Shinoda

  125. United-Atom Acyl Chains for CHARMM Phospholipids

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  129. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants

    Article • Molecular Simulation, January 2007, Taylor & Francis

    Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  132. Molecular Dynamics Study of Bipolar Tetraether Lipid Membranes

    Article • Biophysical Journal, November 2005, Elsevier

    Wataru Shinoda, Wataru Shinoda

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

    Article • Journal of Fluorine Chemistry, October 2005, Elsevier

    Wataru Shinoda, Wataru Shinoda

  134. 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, Wataru Shinoda

  135. 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, Wataru Shinoda

  136. Quantum simulation of the heat capacity of water

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  138. Molecular Dynamics Simulation of Swollen Membrane of Perfluorinated Ionomer

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

    Wataru Shinoda, Wataru Shinoda

  139. 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, Wataru Shinoda

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

    Article • Molecular Simulation, November 2004, Taylor & Francis

    Wataru Shinoda, Wataru Shinoda

  141. 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, Wataru Shinoda

  142. Molecular Dynamics Study on the Effects of Chain Branching on the Physical Properties of Lipid Bilayers:  2. Permeability

    Article • The Journal of Physical Chemistry B, May 2004, American Chemical Society (ACS)

    Wataru Shinoda

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

    Article • Surface Science, May 2004, Elsevier

    Wataru Shinoda, Wataru Shinoda

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

    Article • Chemical Physics Letters, May 2004, Elsevier

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  147. Molecular dynamics study of the Lipid Bilayers: Effects of the Chain Branching on the Structure and Dynamics

    Article • January 2004, American Institute of Physics

    Wataru Shinoda

  148. 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, Wataru Shinoda

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

    Article • Chemical Physics Letters, February 2001, Elsevier

    Wataru Shinoda, Wataru Shinoda

  150. 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, Wataru Shinoda

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

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

    Wataru Shinoda, Wataru Shinoda

  152. 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, Wataru Shinoda