Hiroshi Noguchi

Institute for Molecular Science, Okazaki, Aichi, Japan

Are you Hiroshi Noguchi?

Claim your profile

Publications (9)23.47 Total impact

  • Source
    Bernd A Berg, Hiroshi Noguchi, Yuko Okamoto
    [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.
    Physical Review E 10/2003; 68(3 Pt 2):036126. · 2.31 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The electrophoresis of DNA chains in uncrosslinked polymer solutions with a Brownian dynamics simulation with an anisotropic friction tensor was analyzed. According to the degree of anisotropy, three types of migration behavior are obtained: fluctuation without or with periodicity between U-shaped and compact conformations, or migration with linear conformation. We found good agreement between our simulation results and the direct observations of DNA by fluorescence microscopy. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1316–1322, 2003
    Journal of Polymer Science Part B Polymer Physics 05/2003; 41(12):1316 - 1322. · 2.22 Impact Factor
  • Source
    Hiroshi Noguchi
    [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.
    Physical Review E 05/2003; 67(4 Pt 1):041901. · 2.31 Impact Factor
  • Source
    Hiroshi Noguchi, Masako Takasu
    [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.
    Biophysical Journal 08/2002; 83(1):299-308. · 3.67 Impact Factor
  • Source
    Hiroshi Noguchi, Masako Takasu
    [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.
    Physical Review E 06/2002; 65(5 Pt 1):051907. · 2.31 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
    [Show abstract] [Hide abstract]
    ABSTRACT: We studied the fusion dynamics of vesicles using a Brownian dynamics simulation. Amphiphilic molecules spontaneously form vesicles with a bilayer structure. Two vesicles come into contact and form a stalk intermediate, in which a necklike structure only connects the outer monolayers, as predicted by the stalk hypothesis. We have found a new pathway of pore opening from stalks at high temperature: the elliptic stalk bends and contact between the ends of the arc-shaped stalk leads to pore opening. On the other hand, we have clarified that the pore-opening process at low temperature agrees with the modified stalk model: a pore is induced by contact between the inner monolayers inside the stalk. © 2001 American Institute of Physics.
    The Journal of Chemical Physics 11/2001; 115(20):9547-9551. · 3.12 Impact Factor
  • H Noguchi, M Takasu
    [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.
    Physical Review E 11/2001; 64(4 Pt 1):041913. · 2.31 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
    [Show abstract] [Hide abstract]
    ABSTRACT: We studied the electrophoretic behavior of DNA chains in linear-polymer solutions using Brownian dynamics with an anisotropic friction model in a three-dimensional space and projected on the x axis. For the three-dimensional model with a chain segment equal to 1/8 of the Kuhn length, a chain migrates with U-shaped conformation with low anisotropy of friction. With high anisotropy of friction, a chain always migrates with linear-shaped conformation with high segment-density regions, which remain at the same positions in space. This migration mode agrees with the observation of DNA in highly entangled solutions [Ueda et al., Biophys. Chem. 71, 113 (1998)]. The projection model also reproduces the linear-shaped motion. We clarified that the essential conditions for linear shaped motion are the sufficient chain length of DNA, the small mesh size, and strong confinement by entanglement with solvent polymers. © 2001 American Institute of Physics.
    The Journal of Chemical Physics 04/2001; 114(16):7260-7266. · 3.12 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
    [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.
    Journal of the Physical Society of Japan 01/2000; 69(12):3792-3795. · 2.09 Impact Factor