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Full cover from Science Vol. 321, no. 5890, 8 August 2008. Reprinted with permission from AAAS.
What's New

* New articles
+ Coarse grained model (ionic surfactants)
+Free Energy Calculation for Vesicle-to-Bicelle Transformation

Front cover from PCCP Vol. 9 No. 5, 7 Feb. 2007.


since May 2004

Last updated: July 19, 2013

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Research

Molecular simulation of soft materials ( surfactants, lipids, polymers, peptide ...)

  1. Biological Membranes
    1. Membrane stability and elasticity
    2. Permeability
    3. Lipid mixture
    4. Additives (Cholesterol, alcohol, peptide, etc..)
    5. Membrane proteins
  2. Polymorphism of surfactants
    1. Cubic phase
    2. Confinement effect
    3. Flow effect
  3. Colloidal dispersion
    1. Interactions
    2. Adsorption/desorption of surfactants


Technical development

  1. Multiscale modeling
    1. Coarse-grained molecular model
  2. Free energy methods
  3. Software (MPDyn)
    1. Molecular dynamics
    2. Dissipative particle dynamics

COARSE-GRAIMED MOLECULAR MODEL

We are developping a coarse-grained molecular force field for surfactants and lipids using multi-property fitting as well as distribution functions obtained from all atomic molecular dynamics trajectories. Now the force field for PEG surfactants is available. (See Mol. Simul. 2007, Soft Matter 2008, J. Phys. Chem. B 2010, Soft Matter 2011) Also we are developing CG force field for peptides and RNAs.


PREVIOUS PROJECTS

Quantum effect, isotope effect

  1. Heat capacity of water (path integral molecular dynamics)

Development of simulation techniques

  1. Self-guided molecular dynamics
  2. Hybrid Monte Carlo
  3. Partial rigid-body approximation

Metals

  1. Elastic modulus
  2. Grain boundary

Software

MPDyn MPDyn: A software package for molecular simulations

The MPDyn software is a software package for molecular simulations of various complex materials including polymers, proteins, lipid membranes and so on. Efficient and accurate algorithms are implemented in the program. MPDyn is free software, available under the GNU General Public License.

Simulation tools

  1. Molecular Dynamics (MD)
  2. Hybrid Monte Carlo (HMC)
  3. Dissipative Particle Dynamics (DPD)
  4. Path Integral Molecular Dynamics (PIMD)
  5. Centroid Molecular Dynamics (CMD)
  6. Free energy calculation

Documents & Download


Recent Publications (2003-)

2013

  1. A. Ikeda, M. Ishikawa, R. Aono, J. Kikuchi, M. Akiyama, and W. Shinoda, "Regioselective Recognition of a [60]Fullerene-Bisadduct by Cyclodextrin" J. Org. Chem. 78, 2534 (2013).new!
  2. T. Nakamura and W. Shinoda, "Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory", J. Chem. Phys. 138, 124903 (2013).new!
  3. S. Tsuzuki, W. Shinoda, S. Seki, Y. Umebayashi, K. Yoshida, K. Dokko, and M. Watanabe, "Intermolecular Interactions in Li+-glyme and Li+-glyme-TFSA- complexes: Relationship with Physicochemical Properties of [Li(glyme)][TFSA] Ionic Liquids" ChemPhysChem, 14, 1993(2013).new!s
  4. S. Kawamoto, T. Nakamura, S. O. Nielsen, and W. Shinoda, "A Guiding Potential Method for Evaluating the Bending Rigidity of Tensionless Lipid Membranes from Molecular Simulation" J. Chem. Phys. 139, 034108 (2013).new!

2012

  1. D. LeBard, B. Levine, R. DeVane, W. Shinoda, M. L. Klein, "Premicelles In Aqueous Surfactant Solutions Above and Below the Critical Micelle Concentration" Chem. Phys. Lett. 552, 38 (2012).
  2. W. Shinoda, R. DeVane, M. L. Klein, "Computer Simulation Studies of Self-Assembling Macromolecules" Curr. Opin. Struct. Biol. 22, 175 (2012).
  3. A. Kuo, C. -H. Chang, and W. Shinoda, "Molecular Dynamics Study of Cationic Vesicle Bilayers Composed of Ion Pair Amphiphiles with Double-Tailed Cationic Surfactants", Langmuir, 28, 8156 (2012).
  4. C. -C. Chiu, W. Shinoda, R. DeVane, S. O. Nielsen, "Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach.", Soft Matter, 8, 9610 (2012).
  5. C. -C. Chiu, R. H. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, S. O. Nielsen, "Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach", J. Phys. Chem. C, 116, 23102 (2012).new!
  6. S. Kawamoto, M. Takasu, T. Miyakawa, R. Akiyama, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda, "Free Energy of Cell-Penetrating Peptide through Lipid Bilayer Membrane: Coarse-Grained Model Simulation." Prog. Theo. Chem. Phys. 26, 503 (2012).

2011

  1. A. Jusufi, R. DeVane, W. Shinoda, M. L. Klein, "Nanoscale Carbon Particles and the Stability of Lipid Bilayers", Soft Matter, 7, 1139 (2011).
  2. S. Tsuzuki, H. Matsumoto, W. Shinoda, M. Mikami, "Effects of conformational flexibility of alkyl chain of cations on diffusion of ions in ionic liquids" Phys. Chem. Chem. Phys. 13, 5987 (2011).
  3. W. Shinoda, R. DeVane, M. L. Klein, "Coarse-Grianed Force Field for Ionic Surfactants" Soft Matter, 7, 6178 (2011).
  4. R. J. K. U. Ranatunga, C. T. Nguyen, B. A. Wilson, W. Shinoda, S. O. Nielsen, "Molecular Dynamics Study of Nanoparticles and Nonionic Surfactant at an Oil/Water Interface", Soft Matter, 7, 6942 (2011).
  5. W. Shinoda, T. Nakamura, S. O. Nielsen, "Free Energy Analysis of Vesicle-to-Bicelle Transformation" Soft Matter, 7, 9012 (2011).
  6. T. Nakamura, W. Shinoda, T. Ikeshoji, "Novel Numerical Method for Calculating the Pressure Tensor in Spherical Coordinates for Molecular Systems" J. Chem. Phys. 135, 094106 (2011)..
  7. R. J. K. U. Ranatunga, C. T. Nguen, C. C. Chiu, W. Shinoda, S. O. Nielsen, "Molecular Dynamics Simulations of Nanoparticles and Surfactants at Oil/Water Interfaces- A Qualitative Overview", Chapter 18, pp 295-314, in Amphiphiles: Molecular Assembly and Applications, ACS Synposium Series, Vol 1070, Ed. R. Nagarajan, 2011.
  8. B. Levine, D. LeBard, R. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, "Micellization studied by GPU-accelerated coarse-grained molecular dynamics", J. Chem. Theory Comput. 7, 4135 (2011).
  9. H. Saito and W. Shinoda, "Cholesterol Effect on Water Permeability Through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study" J. Phys. Chem. B 115, 15241 (2011).

2010

  1. T. Nakamura, W. Shinoda, M. Mikami, "The shear hysteresis in lamellar structure of surfactant-water binary system", Chem. Phys. 367, 20 (2010).
  2. C. C. Chiu, R. J. K. U. Ranatunga, D. T. Flores, D. V. Perez, P. B. Moore, W. Shinoda, and S. O. Nielsen, "A mean field approach for computing solid-liquid surface tension for nanoscale interfaces", J. Chem. Phys. 132,054706 (2010).
  3. X. He, W. Shinoda, R. DeVane, K. Andersen, M. L. Klein, "Paramaterization of a Coarse-Grained Model for Linear Alkylbenzene Sulfonate Surfactants and Molecular Dynamics Studies of Their Selfassembly in Aqueous Solution" Chem. Phys. Lett. 487, 71(2010).
  4. R. DeVane, C. C. Chiu, S. O. Nielsen, W. Shinoda, P. B. Moore, and M. L. Klein, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: I. Parametrization" J. Phys. Chem. B, 114, 6386 (2010).
  5. C. C. Chiu, R. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, and S. O. Nielsen, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: II. Application to Fullerenes" J. Phys. Chem. B, 114, 6394 (2010).
  6. W. Shinoda, R. DeVane, M. L. Klein, "Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field." J. Phys. Chem. B, 114, 6836 (2010).
  7. X. He, W. Shinoda, R. DeVane, M. L. Klein, "Exploring the utility of coarse-grained water models for computational studies of interfacial systems" Mol. Phys. 108, 2007 (2010).
  8. S. Tsuzuki, T. Umecky, H. Matsumoto, W. Shinoda, M. Mikami, "Interactions of perfluoroalkyltrifluoroborate anions with Li ion and imidazolium cation: Effects of perfluoroalkyl chain on motion of ions in ionic liquids" J. Phys. Chem. B 114, 11390 (2010).
  9. W. Shinoda, M. Hato, "Molecular Dynamics Study of Isoprenoid-Chained Lipids: Salient Features of Isoprenoid Chains As Compared with Ordinal Alkyl Chains", in "Self-Organized Surfactant Structures", T. F. Tedros Ed., Wiley-Vch, 2010.
  10. R. DeVane, A. Jusufi, W. Shinoda, C. C. Chiu, S. O. Nielsen, P. B. Moore, M. L. Klein, "Parameterization and application of a coarse grained forcefield for benzene/fullerene interactions with lipids" J. Phys. Chem. B, 114, 16364 (2010).

2009

  1. U. O. M. Vazquez, W. Shinoda, P. B. Moore, C. C. Chiu, S. O. Nielsen, "Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods." J. Math. Chem. 45 161(2009)..
  2. R. J. B. Kalescky, W. Shinoda, P. B. Moore, S. O. Nielsen, "Area per ligand as a function of nanoparticle radius: a theoretical and computer simulation approach", Langmuir, 25, 1352 (2009).
  3. R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein, "Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids" J. Chem. Theory Comput. 5, 2115 (2009).
  4. C. C. Chiu, P. B. Moore, W. Shinoda, S. O. Nielsen, "Size-dependent hydrophobic to hydrophilic transition for nanoparticles: a molecular dynamics study", J. Chem. Phys. 131, 244706 (2009).
  5. H. Saito, W. Shinoda, M. Mikami, "Fluorination Effects on Structure and Dynamics of Phospholipid Bilayer: A Molecular Dynamics Study" Chem. Phys. Lett. 468, 260 (2009).
  6. J. Henin, W. Shinoda, and M. L. Klein, "Models for phospatidylglycerol lipids put to structural test." J. Phys. Chem. B, 113, 6958 (2009).
  7. S. Tsuzuki, W. Shinoda, H. Saito, M. Mikami, H. Tokuda, and M. Watanabe, J. Phys. Chem. B 113, 10641 (2009).

2008

  1. M. L. Klein and W. Shinoda, "Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems" Science, 321, 798 (2008)
    Full cover from Science Vol. 321, no. 5890, 8 August 2008. Reprinted with permission from AAAS.
  2. W. Shinoda, R. DeVane, M. L. Klein, "Coarse-grained molecular modeling of nonionic surfactant self-assembly" Soft Matter, 4, 2454 (2008).
  3. W. Shinoda, R. DeVane, M. L. Klein, "Self-assembly of Surfactants in Bulk Phases and at Interfaces using Coarse-grain Models", Chapter 22 of the book "Coarse-Graining of Condensed Phase and Biomolecular Systems", G. A. Voth Ed., CRC Press, 2008.
  4. K. Shinoda, W. Shinoda, M. Mikami, "Efficient free energy calculation of water across lipid membranes." J. Comput. Chem. 29, 1912 (2008).
  5. J. Hénin, W. Shinoda, and M. L. Klein, "United-atom acyl chains for CHARMM phospholipids." J. Phys. Chem. B 112, 7008 (2008).
  6. N. Matubayasi, W. Shinoda, M. Nakahara, "Free-energy analysis of the binding into membrane with the method of energy representation." J. Chem. Phys. 128, 195107 (2008).
  7. H. Saito, W. Shinoda, M. Mikami, "Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study" J. Phys. Chem. B 112, 11305 (2008).
  8. K. Nishio, T. Ozaki, T. Morishita, W. Shinoda, M. Mikami, "Effects of encapsulating sodium and iodine atoms on the electronic and optical properties of polyicosahedral Si nanostructures: a first-principles study" Phys. Rev. B 77 075431(2008).

2007

  1. W. Shinoda, R. DeVane, M. L. Klein, "Multi-property Fitting and Parameterization of a Coarse Grained Model for Aqueous Surfactants", Mol. Simul. 33 27(2007).
  2. K. Shinoda, W. Shinoda, M. Mikami, "Molecular dynamics simulation of archaeal lipid bilayer with sodium chloride." Phys. Chem. Chem. Phys. 9 643 (2007).
    Front cover from PCCP Vol. 9 No. 5, 7 Feb. 2007.

2006

  1. K. Nishio, T. Morishita, W. Shinoda and M. Mikami, "Molecular dynamics simulations of self-organized polyicosahedral Si nanowire." J. Chem. Phys. 125 074712 (2006).

2005

  1. W. Shinoda, K. Shinoda, T. Baba, and M. Mikami, "Molecular dynamics study of bipolar tetraether membranes." Biophys. J. 89 3195 (2005).
  2. W. Shinoda and M. Shiga, "Quantum simulation of the heat capacity of water." Phys. Rev. E 71 041204 (2005).
  3. M. Shiga and W. Shinoda, "Calculation of heat capacities of light and heavy water by path integral molecular dynamics." J. Chem. Phys. 123 134502 (2005).
  4. K. Nishio, T. Morishita, W. Shinoda , and M. Mikami, "Formation of Icosahedral Si Quantum Dots from Liquid Droplets." Phys. Rev. B 72 245321 (2005).
  5. K. Nishio, W. Shinoda, T. Morishita, and M. Mikami, "Spatial Confinement Effect on the Atomic Structure of Solid Argon." J. Chem. Phys. 112 124715 (2005).
  6. S. Urata, J. Irisawa, A. Takada, W. Shinoda, S. Tsuzuki, and M. Mikami, "Molecular Dynamics Simulation of Swollen Membrane of Perfluorinated Ionomer." J. Phys. Chem. B 109, 4269 (2005).
  7. S. Urata, J. Irisawa, A. Takada, W. Shinoda, S. Tsuzuki, and M. Mikami, "Molecular Dynamics Study of the Methanol Effect on the Membrane Morphology of Perfluorosulfonic Ionomer" J. Phys. Chem. B 109 17274 (2005).
  8. S. Urata, J. Irisawa, A. Takada, S. Tsuzuki, W. Shinoda, and M. Mikami, "Intermolecular interaction between the pendant chain of perfluorinated ionomer and methanol." J. Fluorine Chem. 126 1312 (2005).

2004

  1. B. Hafskjold, C. C. Liew, and W. Shinoda, "Can such long time steps really be used in dissipative particle dynamics simulations?" Mol. Simul. 30, 879 (2004).
  2. W. Shinoda, M. Shiga, and M. Mikami, "Rapid estimation of elastic constants by molecular dynamics simulation under constant stress." Phys. Rev. B 69, 134103 (2004).
  3. M. Shiga and W. Shinoda, "Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study", Phys. Rev. B 70, 054102 (2004).
  4. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers: 2. Permeability." J. Phys. Chem. B 108 9346 (2004).
  5. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Dynamics of a highly branched lipid bilayer: A molecular dynamics study." Chem. Phys. Lett. 390, 35 (2004).
  6. K. Shinoda, W. Shinoda, T. Baba, and M. Mikami, "Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers." J. Chem. Phys. 121 9648 (2004).
  7. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study of the lipid bilayers: Effects of the chain branching on the structure and dynamics" AIP Conference series, 708, 352 (2004).
  8. K. Shinoda, W. Shinoda, C. C. Liew, S. Tsuzuki, Y. Morikawa, and M. Mikami, "Two-dimensional self-assembled structures of adenine molecules: Modeling and simulation." Surf. Sci. 556, 109 (2004).
  9. K. Shinoda, W. Shinoda, C. C. Liew, S. Tsuzuki, Y. Morikawa, and M. Mikami, "Mechanism of two-dimensional superstructure formation of self-assembled adenine molecules." Transactions of the Materials Research Society of Japan, 29, 3755 (2004).
  10. S. Urata, J. Irisawa, A. Takada, S. Tsuzuki, W. Shinoda, and M. Mikami, "Intermolecular interaction between the pendant chain of perfluorinated ionomer and water." Phys. Chem. Chem. Phys. 6, 3325 (2004).

2003

  1. W. Shinoda and M. Mikami, "Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency." J. Comput. Chem. 24, 920 (2003).
  2. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study on the effect of chain branching on the physical properties of lipid bilayers: Structural stability." J. Phys. Chem. B 107, 14030 (2003).
  3. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "A comparison of straight- and branch-chained lipid bilayers for static and dynamic properties: A molecular dynamics study" Technical Proceedings of the 2003 Nanotechnology Conference and Trade ShowC3C512 (2003).

2001

  1. W. Shinoda and M. Mikami, "Self-guided molecular dynamics in the isothermal-isobaric ensemble", Chem. Phys. Lett. 335 265 (2001).
  2. W. Shinoda and S. Okazaki, "Molcular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: An effect of potential force field on the membrane structure." J. Mol. Liq. 90 95 (2001).

-1999

  1. Z. Fang, A. D. J. Haymet, W. Sihnoda, and S. Okazaki, "Parallel molecular dynamics simulation: implementation of PVM for a lipid membrane", Comput. Phys. Comm. 116, 295 (1999).
  2. W. Shinoda, M. Shimizu, and S. Okazaki, "Molecular dynamics study on electrostatic properties of the lipid bilayer : Polarization, electrostatic potential, and the effects on structure and dynamics of water near the interface." J. Phys. Chem. B 102 6647 (1998).
  3. W. Shinoda and S. Okazaki, "A Voronoi analysis of lipid area fluctuation in a bilayer." J. Chem. Phys. 109 1517 (1998).
  4. W. Shinoda, N. Namiki, and S. Okazaki, "Molecular dynamics study of a lipid bilayer. Convergence, structure, and long-time dynamics." J. Chem. Phys. 106 5731(1997).
  5. W. Shinoda, T. Fukada, S. Okazaki, and I. Okada, "Molecular dynamics simulation of the dipalmitoylphosphatidylcholine(DPPC) lipid bilayer in the fluid phase using the Nose-Parrinello-Rahman NPT ensemble." Chem. Phys. Lett. 232 308 (1995).

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