[Show abstract][Hide abstract] ABSTRACT: We introduce a procedure to construct weight factors, which flatten the probability density of the overlap with respect to some predefined reference configuration. This allows one to overcome free-energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brain peptide Met-enkephalin with the ECEPP/2 (Empirical Conformational Energy Program for Peptides) energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free-energy barrier.
[Show abstract][Hide abstract] ABSTRACT: Polyhedral vesicles with a large bending modulus of the membrane, such as a gel phase lipid membrane, were studied using a Brownian dynamics simulation. The vesicles exhibited various polyhedral morphologies such as tetrahedron and cube shapes. We clarified two types of line defects on the edges of the polyhedrons: cracks of both monolayers at the spontaneous curvature of the monolayer C0<0, and a crack of the inner monolayer at C0> or =0. The inner monolayer curved positively around the latter defect. Our results suggest that the polyhedral morphology is controlled by C0.
[Show abstract][Hide abstract] ABSTRACT: We studied the interaction of bilayer vesicles and adhesive nanoparticles using a Brownian dynamics simulation. The nanoparticles are simple models of proteins or colloids. The adhering nanoparticle induces the morphological change of the vesicle: budding, formation of two vesicles in which only outer monolayers are connected, and fission. We also show that the nanoparticle promotes the fusion process: fusion-pore opening from a stalk intermediate, a neck-like structure that only connects outer monolayers of two vesicles. The nanoparticle bends the stalk, and induces the pore opening.
Preview · Article · Aug 2002 · Biophysical Journal
[Show abstract][Hide abstract] ABSTRACT: We studied the structural changes of bilayer vesicles induced by mechanical forces using a Brownian dynamics simulation. Two nanoparticles, which interact repulsively with amphiphilic molecules, are put inside a vesicle. The position of one nanoparticle is fixed, and the other is moved by a constant force as in optical-trapping experiments. First, the pulled vesicle stretches into a pear or tube shape. Then the inner monolayer in the tube-shaped region is deformed, and a cylindrical structure is formed between two vesicles. After stretching the cylindrical region, fission occurs near the moved vesicle. Soon after this the cylindrical region shrinks. The trapping force approximately 100 pN is needed to induce the formation of the cylindrical structure and fission.
[Show abstract][Hide abstract] ABSTRACT: We studied the vesicles of amphiphilic molecules using a Brownian dynamics simulation. An amphiphilic molecule is modeled as the rigid rod, and the hydrophobic interaction is mimicked by the local density potential of the hydrophobic particles. The amphiphilic molecules self-assemble into vesicles with bilayer structure. The vesicles are in fluid phase, and we calculated the lateral diffusion constant and the rate of the flip-flop motion of molecules in vesicles. The self-assembly kinetics into vesicles was also investigated.
No preview · Article · Nov 2001 · Physical Review E
[Show abstract][Hide abstract] ABSTRACT: We studied the electrophoretic behavior of DNA chains in linear-polymersolutions using Brownian dynamics with an anisotropic friction tensor.We simulated the linear-shaped motion of DNA observed in highlyentangled solutions [Ueda et al.: Biophys. Chem. 71 (1998) 113] using a model with a chain segment equal to 1/4 of the persistence length. A linear conformation is seen for a chain with high segment-density regions, which remain at the same positions in space, with a high anisotropy of friction, while a U-shaped conformation is seen for a chain with a low anisotropy of friction.
No preview · Article · Dec 2000 · Journal of the Physical Society of Japan
[Show abstract][Hide abstract] ABSTRACT: We have studied the dynamical behavior of a polymer chain with double minima in the free energy, bathing in an isothermal environment with an external energy supply. Under the theoretical framework that the free energy depends on the degree of energization in the chain, we show that these molecular chains show a limit-cycle oscillation. Such dynamic characteristics are discussed in relation to the functions of working proteins as the molecular machinery of life.
No preview · Article · Apr 1999 · Chemical Physics Letters
[Show abstract][Hide abstract] ABSTRACT: We studied the thermodynamics in a single homopolymer chain using a multicanonical Monte Carlo simulation. A polymer chain that exhibits an elongated coil state in a good solvent, or at high temperatures, collapses into a condensed state, i.e., coil-globule transition. For flexible polymer chains, as the temperature decreases, the coil state changes into a liquidlike spherical globule, and this liquid state then changes into a solidlike spherical globule; these are similar to the transitions between gas and liquid and between liquid and solid, respectively. For stiff polymer chains, the coil state changes into a crystalline state without the appearance of an intermediate liquidlike state, to give a product with toroidal morphology. For chains intermediate between stiff and flexible, the coil state changes into a state in which toroid and rod shapes coexist, and this state changes into a single solidlike state in which only the rod shape is present. These calculational results correspond well to experimental findings for the products of the collapse of single long DNA chains.
Full-text · Article · Sep 1998 · The Journal of Chemical Physics
[Show abstract][Hide abstract] ABSTRACT: We studied the transition between the elongated coil and collapsed globule states in a single polymer chain, avoiding kinetic effects such as supercooling, or kinetic trapping into local minima, using a multicanonical method. It has become clear that single stiff chains exhibits a first-order phase transition. Reflecting the finiteness of the number of elements (or the number of segments) in a chain, the two states, coil and globule, coexist within a finite width of temperature for the ensemble of monodisperse chains, even under true thermodynamic equilibrium.
No preview · Article · Oct 1997 · Chemical Physics Letters
[Show abstract][Hide abstract] ABSTRACT: A Monte Carlo simulation was performed on the folding transition of a single stiff polymer chain. We have adapted a polymer model: neighboring beads are connected by a stick and the length of each stick is taken as 18 of the Kuhn length. Among the products of the folding from the single chain, the toroidal structure is found to be the most stable. Rod and fused structures between rod and toroid are also generated as metastable states with almost infinite lifetime. These morphologies resemble the experimental structures observed with electron microscopy for the products of collapse from single duplex DNA chains.
No preview · Article · Oct 1996 · Chemical Physics Letters