Toshihiro Kawakatsu

Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

Self-Assembly of Triton X-100 in Water Solutions: A Multiscale Simulation Study Linking Mesoscale to Atomistic Models

A multiscale scheme is proposed and validated for Triton X-100 (TX-100), which is a detergent widely employed in biology. The hybrid particle field formulation of the model allows simulations of large-scale systems. The coarse-grained (CG) model, accurately validated in a wide range of concentrations, shows a critical micelle concentration, shape transition in isotropic micellar phase, and appearance of hexagonal ordered phase in the experimental ranges reported in the literature. The fine resolution of the proposed CG model allows one to obtain, by a suitable reverse mapping procedure, atomistic models of micellar assemblies and of the hexagonal phase. In particular, atomistic models of the micelles give structures in good agreement with experimental pair distance distribution functions and hydrodynamic measurements. The picture emerging by detailed analysis of simulated systems is quite complex. Polydisperse mixtures of spherical-, oblate-, and prolate-shaped aggregates have been found. The shape and the micelle behavior are mainly dictated by the aggregation number (Nagg). Micelles with low Nagg values (∼40) are spherical, while those with high Nagg values (∼140 or larger) are characterized by prolate ellipsoidal shapes. For intermediate Nagg values (∼70), fluxional micelles alternating between oblate and prolate shapes are found. The proposed model opens the way to investigations of several mechanisms involving TX-100 assembly in protein and membrane biophysics.

Soft confinement for polymer solutions

As a model of soft confinement for polymers, we investigated equilibrium shapes of a flexible vesicle that contains a phase-separating polymer solution. To simulate such a system, we combined the phase field theory (PFT) for the vesicle and the self-consistent field theory (SCFT) for the polymer solution. We observed a transition from a symmetric prolate shape of the vesicle to an asymmetric pear shape induced by the domain structure of the enclosed polymer solution. Moreover, when a non-zero spontaneous curvature of the vesicle is introduced, a re-entrant transition between the prolate and the dumbbell shapes of the vesicle is observed. This re-entrant transition is explained by considering the competition between the loss of conformational entropy and that of translational entropy of polymer chains due to the confinement by the deformable vesicle. This finding is in accordance with the recent experimental result reported by Terasawa, et al.

Thinning Approximation for Two-Dimensional Scattering Patterns from Coarse-Grained Polymer Melts under Shear Flow

We proposed a thinning approximation (TA) for estimation of the two-dimensional (2D) wide-angle scattering patterns from Kremer–Grest polymer melts under shear. In the TA, extra particles are inserted at the middle of bonds for fine-graining of the coarse-grained polymers. For the case without the TA, spots corresponding to the orientation of bonds at a high shear rate are difficult to observe because the bond length of successive particles is comparable to the distance between neighboring particles. With the insertion of the extra particles, a ring pattern originating from the neighboring particles can be moved to a wide-angle region. Thus, we can observe the spots at high shear rates. We also examined the relationship between 2D scattering patterns and the Weissenberg number, which is defined as the product of the shear rate and the longest relaxation time. It is confirmed that the relationship for coarse-grained polymers with the TA is consistent with that of the all-atomistic model of polyethylene.

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment

We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al. Phys. Chem. Chem. Phys. 2016 , 18 , 9799 ]. Our results show that, upon proper calibration of key parameters, electrostatic forces can be correctly reproduced. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. The inclusion of explicit electrostatics with good accuracy and low computational cost paves the way for a significant extension of the hybrid particle-field method to biological systems, where the polyelectrolyte component plays a fundamental role for both structural and dynamical molecular properties.

Translocation of a vesicle through a narrow hole across a membrane

We study the translocation process of a vesicle through a hole in a solid membrane separating two chambers by using the Onsager principle. By considering the stretching energy of the vesicle and the driving force due to pressure difference, we derive a free energy that shows clearly a decrease in the energy barrier as the pressure difference between two sides of the membrane increases. The difference between the reaction path obtained from the string method and the actual kinetic paths obtained from the Onsager principle is discussed when the friction parameter changes. The translocation time decreases as the pressure difference increases or the initial size of the vesicle decreases.

Onsager’s variational principle for the dynamics of a vesicle in a Poiseuille flow

We propose a systematic formulation of the migration behaviors of a vesicle in a Poiseuille flow based on Onsagers variational principle, which can be used to determine the most stable steady state. Our model is described by a combination of the phase field theory for the vesicle and the hydrodynamics for the flow field. The dynamics is governed by the bending elastic energy and the dissipation functional, the latter being composed of viscous dissipation of the flow field, dissipation of the bending energy of the vesicle, and the friction between the vesicle and the flow field. We performed a series of simulations on 2-dimensional systems by changing the bending elasticity of the membrane and observed 3 types of steady states, i.e., those with slipper shape, bullet shape, and snaking motion, and a quasi-steady state with zig-zag motion. We show that the transitions among these steady states can be quantitatively explained by evaluating the dissipation functional, which is determined by the competition between the friction on the vesicle surface and the viscous dissipation in the bulk flow.

A minimal model of collective behaviour based on non-reciprocal interactions.

The collective behaviour of individuals is widely observed in many natural and social systems. In these systems, Newton’s third law, or the law of action–reaction, is often violated. Hence, interac...

Orientation-shape coupling between liquid crystal and membrane through the anchoring effect

We perform a series of Monte Carlo simulations on an interface between a liquid crystal (LC) material in isotropic phase in its bulk and a surfactant membrane. These two objects are simulated using coarse-grained molecular models. We estimate physical properties of the membrane such as the interfacial tension and the bending rigidity, focusing on the anchoring effects of the membrane on the LC. According to our simulation results, when the strength of the homeotropic anchoring denoted by the anchoring parameter ξ is increased, the interfacial tension decreases and the bending rigidity first increases in ξ<ξ_{m}, and it then decreases in ξ_{m}<ξ. We explain these results by constructing a continuum field model based on the two order parameters: directional order of LC and the membrane shape. These order parameters are mutually interacting through the anchoring effect, the fluctuation coupling between the LC and the membrane, and the effect of the nematic layer.