Nagoya University · Biochemistry, Genetics and Molecular Biology
Professor Wataru Shinoda's research lab specializes in computational materials science and molecular simulation, focusing on the development and application of advanced coarse-grained (CG) models for complex soft matter systems such as surfactants, lipids, and self-assembled nanostructures. The lab emphasizes the creation of transferable and accurate CG force fields that reproduce key thermodynamic and structural properties from all-atom simulations, with applications in interfacial phenomena, membrane biophysics, and self-assembly in complex fluids. They also pioneer novel simulation algorithms—such as efficient NPT molecular dynamics with rigid bodies and enhanced sampling techniques—to improve the accuracy and efficiency of molecular simulations. Their work bridges fundamental simulation methodology with practical applications in materials design and biological systems.
Figures are computed from collected data and may differ slightly.
Molecular simulations, when they are used to understand properties characterizing the mechanical strength of solid materials, such as stress-strain relation or Born stability criterion, by using elastic constants, are sometimes seriously time consuming. In order to resolve this problem, we propose an efficient simulation approach under constant external stress and temperature, modifying Parrinello-Rahman (PR) method using useful sampling techniques developed recently---massive Nos\'e-Hoover chai
A new systematic approach to build coarse-grained (CG) molecular models for surfactants/water systems is proposed. A step-by-step approach using several molecular systems for the parameterization makes the CG model versatile and transferable. The intramolecular bond potentials are determined to reproduce the bond and angle distributions obtained from all-atom (AA) molecular dynamics (MD) simulations. A careful choice of the potential function for nonbonded interactions is essential for better st
Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.
A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable mo
A coarse-grained (CG) molecular model for nonionic surfactants is presented. The transferability and versatility are demonstrated by applying the model to the bulk aqueous solution as well as to the air–water and oil–water interfacial systems. The model is designed to reproduce several key properties including surface/interfacial tension, bulk density, compressibility, hydration/transfer free energy as well as distribution functions obtained by all-atom molecular dynamics simulations. The CG sur
We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and ef
We studied the effects of chain branching on the water and nonionic (neutral) solute permeability of lipid bilayers in a molecular dynamics simulation comparing two bilayers: dipalmitoylphosphatidylcholine (DPPC) and diphytanoylphosphatidylcholine (DPhPC). The calculated free energy profiles of several neutral solute and water molecules across the lipid membranes showed that chain branching caused no significant changes in the solubility of these molecules inside the membrane core. However, an a
Heterogeneity is essential for multicomponent lipid membranes. Especially, sterol-induced domain formation in membranes has recently attracted attention because of its biological importance. To investigate such membrane domains at the molecular level, coarse-grained molecular dynamics (CG-MD) simulations are a promising approach since they allow one to consider the temporal and spatial scales involved in domain formation. In this work, we present a new CG force field, named SPICA, which can accu
Membrane area fluctuation of the lipid bilayer has been investigated based upon two-dimensional Voronoi tessellation analysis for the centers of mass of the lipid molecules projected on the bilayer plane. Long-time trajectories of the molecules used in the analysis have been generated by molecular dynamics calculations. The single-molecular area defined by Voronoi polygon showed a broad Gaussian distribution, from which area distribution of the membrane composed of N lipid molecules may satisfac
We present a new coarse-grained (CG) molecular model for ionic surfactants, which is compatible with previously developed CG models for nonionic surfactants and lipids. The CG force field is described by rather simple interaction functions including a separate non-truncated Coulomb interaction term between charged segments. The CG surfactant model reproduces experimental surface tension and density as well as distribution functions from all-atomic molecular models. A CG molecular dynamics simula
The free energy profile of the stalk model of membrane fusion has been calculated using coarse-grained molecular dynamics simulations. The proposed method guides the lipid configuration using a guiding wall potential to make the transition from two apposed membranes to a stalk and a fusion pore. The free energy profile is obtained with a thermodynamic integration scheme using the mean force working on the guiding wall as a response of the system. We applied the method to two apposed flat bilayer
Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nosé-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such as atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structu
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