Susumu Fujiwara

Molecular dynamics simulations of structural formation of a single polymer chain: Bond-orientational order and conformational defects

The structural formation of a single polymer chain with 500 CH2 groups is studied by the molecular dynamics simulations. Our simulations show that the bond-orientationally ordered structure at low temperatures is formed from a random-coil structure at high temperatures by a gradual stepwise cooling. From the radii of gyration and the bond-orientational order parameters, it is found that the anisotropy of a polymer chain also grows during the growth of the bond-orientational order. In the bond-orientationally ordered structure at low temperatures, 16 stems form a structure with deformed hexagonal symmetry and the stems in the outer layer have a tilted configuration. Furthermore, the gauche states are localized in the fold surface and the conformational states in the fold surface change more readily than those in the orientationally-ordered region.

Molecular dynamics simulation of structure formation of short chain molecules

Molecular dynamics simulations are carried out to study the structure formation of 100 short chain molecules, each of which consists of 20 CH2 groups. Our simulations show that the orientationally ordered structure is formed from a random configuration by quenching. The global orientational order starts to increase suddenly after a certain duration and grow in a stepwise fashion afterwards. This behavior is also found in the growth process of the local orientationally-ordered domains. It is found from the microscopic analysis of the structure formation process, that parallel ordering of chain molecules starts to occur after the chain molecules stretch to some extent. From the analysis of the obtained orientationally ordered structure and the molecular mobility, we also find the following characteristic features: (i) The chain molecules are packed hexagonally at 400 K and the transition from the hexagonal phase toward the orthorhombic phase takes place as the temperature decreases. (ii) The gauche bonds in...

Structure formation of a single polymer chain. I. Growth of trans domains

Molecular dynamics simulations are carried out to study structure formation of a single polymer chain with 500 CH2 groups. Our simulations show that the orientationally ordered structure is formed at a low temperature both by gradual stepwise cooling and by quenching from a random configuration at a higher temperature. The growth of the global orientational order proceeds in a gradual manner in the case of gradual stepwise cooling, whereas it proceeds in a stepwise manner in the case of quenching. The latter feature endorses the previously proposed hypothetical grand view of self-organization [e.g., see T. Sato, Phys. Plasmas 3, 2135 (1996)]: when a system is driven far from equilibrium, it will evolve to a more stable state in a stepwise fashion irrespective of its fundamental interaction forces. From the microscopic analysis of the structure formation process, we find the following characteristic features: (i) In the case of gradual stepwise cooling, the global orientational order grows gradually throug...

Molecular dynamics simulation of amphiphilic molecules in solution : Micelle formation and dynamic coexistence

The micelle formation and the dynamic coexistence in amphiphilic solution are investigated by molecular dynamics simulation of coarse-grained rigid amphiphilic molecules with explicit solvent molecules. Our simulations show that three kinds of isolated micelles (disk, cylindrical, and spherical micelles) are observed at a lower temperature by quenching from a random configuration of amphiphilic molecules in solution at a higher temperature. The micellar shape changes from a disk into a cylinder, and then into a sphere as the hydrophilic interaction increases whereas it is not so sensitive to the variation of the hydrophobic interaction. This fact indicates that the hydrophilic interaction plays an important role in determining the micellar shape in the range of the interaction parameters used. It is also found that in a certain interaction parameter range, two kinds of micellar shapes coexist dynamically. From the detailed analyses of the dynamic coexistence, it is ascertained that the dynamic coexistence of a cylindrical micelle and a spherical micelle accompanies the coalescence and fragmentation of micelles while that of a disk micelle and a cylindrical micelle does not, but exhibits the continuous change between them.

Molecular dynamics simulation of micelle formation in amphiphilic solution

The micelle formation in amphiphilic solution is investigated by molecular dynamics (MD) simulation of coarse-grained rigid amphiphiles with explicit solvent molecules. In our simulation model, the intensity of the hydrophilic interaction and the hydrophobic interaction can be varied independently. Our simulations show that various kinds of micellar structures are formed at a lower temperature by quenching from a random configuration of amphiphilic molecules in solution at a higher temperature. The micellar shape changes from a disc (bilayer) into a cylinder and then into a sphere as the intensity of the hydrophilic interaction increases. It is also found that the micelle formation proceeds in a stepwise fashion through the coalescence of smaller micelles. From the analysis of the orientational order for the amphiphilic molecules, it is concluded that the orientational order parameters can be used to distinguish the micellar shapes clearly.

Molecular dynamics simulation of self-organization in amphiphilic solution

The micelle formation in amphiphilie solution is investigated by means of a a molecular dynamics simulation of coarse-grained amphipliilic molecules with explicit solvent molecules. A random configuration of amphiphilic molecules in solution at high temperature is quenched to a lower temperature. Our simulations show that the micella shapes change from a cylindrical micelle to a planar bilayer as the number density increases. At higher densities, we also find the following characteristic features. (1) The potential energy relaxes in a stepwise manner (2) The radius of gyration R g of the largest micelles increases with time in a stepwise fashion, (3) The sharp bumps in R g occur during coalescence of micelles.

Gradient pattern analysis of structural dynamics: application to molecular system relaxation

This paper describes an innovative technique, the gradient pattern analysis (GPA), for analysing spatially extended dynamics. The measures obtained from GPA are based on the spatio-temporal correlations between large and small amplitude fluctuations of the structure represented as a dynamical gradient pattern. By means of four gradient moments it is possible to quantify the relative fluctuations and scaling coherence at a dynamical numerical lattice and this is a set of proper measures of the pattern complexity and equilibrium. The GPA technique is applied for the first time in 3D-simulated molecular chains with the objective of characterizing small symmetry breaking, amplitude and phase disorder due to spatio-temporal fluctuations driven by the spatially extended dynamics of a relaxation regime.

Molecular Dynamics Simulation for Structure Formation of Single Polymer Chain in Solution

The structure formation of a single polymer chain in solution with explicit solvent molecules is investigated by molecular dynamics simulation. The orientationally ordered structure is formed at a low temperature by quenching from a random conformation at a high temperature. The growth of the global and local orientational order proceeds in a stepwise manner at T ≥350 K, whereas it proceeds in a gradual manner at T =300 K. From the detailed analyses of the parallel ordering process, it is found that a conformational change of the polymer chain occurs at first, and then parallel ordering starts to take place. In comparison with the simulation results of an isolated polymer chain in vacuum, it is ascertained that the stem length of the orientationally ordered structure formed in solution becomes 2–3 times longer than that formed in vacuum.

Molecular dynamics study of structure formation of a single polymer chain by cooling

Structure formation of a single polymer chain with 500 methylene groups is investigated by means of a molecular dynamics simulation. We find that the folded orientationally ordered structure is formed at a low temperature by gradual stepwise cooling or by quenching from a random configuration at a higher temperature. It is also found that the global orientational order grows in a gradual manner in the case of gradual stepwise cooling, whereas it grows in a stepwise manner in the case of quenching.

Molecular Dynamics Study of the Structural Formation of Short Chain Molecules: Structure and Molecular Mobility

Abstract By carrying out molecular dynamics simulations of 100 short chain molecules, each of which consists of 20 CH2 groups, we show that the orientationally ordered structure is formed at low temperature by a sudden cooling from a random configuration at high temperature. The essentially extended chains form a monolayer structure. The ratio of the lattice constants a/b takes the hexagonal value ∼3 at 400 K and decreases as the temperature decreases. From detailed analysis of the local orientational order, it is found that the growth of the local ordered clusters proceeds in a stepwise fashion. From the analysis of the molecular mobility, we find that the longitudinal chain motion increases dramatically with increasing temperature while the transverse chain motion is not sensitive to the temperature variation.