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MSSI/Bernal Institute Research Forum - Wednesday, 28 September at 11h00

MSSI/Bernal Institute Research Forum - Wednesday, 28 September at 11h00


Dr Wataru Shinoda, Department of Applied Chemistry, Nagoya University, Japan


Coarse-Grained Molecular Dynamics of Macromolecular Self-Assembly


A recent development of our coarse-grained (CG) molecular model using a multi-property fitting approach will be presented. The CG model (known as the SDK CG model) is designed to reproduce experimental surface/interfacial properties of molecular assembly as well as distribution functions from all-atom molecular dynamics (MD) simulations using the CHARMM force field.[1] This bottom-up approach works well for lipids and surfactants self-assemblies, [1] and the CG model has been extended to include sterols, proteins, nanoparticles, and polymers.[2] This presentation mainly shares our CG-MD results of membrane systems subject to large morphological and topological changes.[3] A comparison of the CG-MD results with the conventional continuum model based on the Helfrich Hamiltonian has also been made. The effects of lipid components and additives such as nanoparticles and peptides will also be discussed.

[1]     Shinoda, W.; DeVane, R.; Klein, M.L. Mol. Simulat. 2007, 33, 27–36: Soft Matter, 2008, 4, 2454-2462: J. Phys. Chem. B, 2010, 114, 6836-6849: Soft Matter, 2011, 7, 6178-6186.

[2]     DeVane, R. et al., J. Chem. Theory Comput. 2009, 5, 2115-2124: DeVane R. et al., J. Phys. Chem. B, 2010, 114, 16364-16372: MacDarmaid, C. et al., J. Chem. Phys. 2015, 143, 243144.

[3]     Kawamoto, S. et al., Soft Matter, 2014, 10, 3048-3054: J. Chem. Phys. 2015, 143, 243112.


Dr Wataru Shinoda is Associate Professor in the Department of Applied Chemistry at Nagoya University, Japan. His group uses molecular simulation techniques to understand and predict various functions of molecules and molecular assemblies such as lipid membranes, aiming to inform the design of new materials. In order to tackle technical issues in bio- and soft-materials, they utilize multi-scale molecular modeling, ranging from sub-atomic scales of quantum mechanics, to the coarse-grained molecular level, reaching to the micron scale. By developing these simulation techniques and applying them to contemporary problems, they expand the frontiers of molecular simulations. Dr Shinoda has published in a variety of journals including Science.

DATE:           Wednesday, 28 September 2016

TIME:            11h00

VENUE:        MSG-025 MSSI Building Extension


For further information, please contact: damien.thompson@ul.ie