Hiroshi Noguchi

Kyoto University, Kyoto, Kyoto-fu, Japan

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Publications (16)41.86 Total impact

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    Bernd A Berg, Hiroshi Noguchi, Yuko Okamoto
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    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. DOI:10.1103/PhysRevE.68.036126 · 2.33 Impact Factor
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    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 06/2003; 41(12):1316 - 1322. DOI:10.1002/polb.10458 · 2.55 Impact Factor
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    Hiroshi Noguchi
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    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. DOI:10.1103/PhysRevE.67.041901 · 2.33 Impact Factor
  • Hiroshi Noguchi
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    ABSTRACT: We studied the morphological change in bilayer vesicles induced by mechanical forces using a Brownian dynamics simulation. When bilayer membranes in two vesicles or the same vesicle are pushed from both sides by two nanoparticles, they fuse into a spherical or toroidal vesicle, respectively. Under large forces, the fusion occurs directly after the contact of the distal (trans) monolayers. Stochastically, a fusion intermediate, a disk-shaped bilayer consisting of both inner monolayers is formed under weaker forces. In this intermediate, the fusion pore that connects the insides of the vesicles is formed at the edge of the bilayer disk. These fusion processes are different from those of spontaneous fusion. The toroidal vesicle spontaneously changes back into a spherical shape, because the vesicle is small. The hole of the toroid disappears through a cylindrical stalk. © 2002 American Institute of Physics.
    The Journal of Chemical Physics 10/2002; 117(17):8130-8137. DOI:10.1063/1.1510114 · 3.12 Impact Factor
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    Hiroshi Noguchi, Masako Takasu
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    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. DOI:10.1016/S0006-3495(02)75170-9 · 3.83 Impact Factor
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    Hiroshi Noguchi, Masako Takasu
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    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. DOI:10.1103/PhysRevE.65.051907 · 2.33 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
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    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. DOI:10.1063/1.1414314 · 3.12 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
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    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. DOI:10.1103/PhysRevE.64.041913 · 2.33 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
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    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. DOI:10.1063/1.1359481 · 3.12 Impact Factor
  • Hiroshi Noguchi, Masako Takasu
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    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 12/2000; 69(12):3792-3795. DOI:10.1143/JPSJ.69.3792 · 1.48 Impact Factor
  • Hiroshi Noguchi, Kenichi Yoshikawa
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    ABSTRACT: We studied the kinetics of the folding transition of a semiflexible homopolymer chain, such as DNA, using a Brownian dynamics simulation. The folding product of a semiflexible chain exhibits a toroidal morphology. We show that semiflexible chains fold through various paths from coiled states to toroidal states stochastically. Some chains fold directly by winding around a ring along a chain. Others fold through rod states, which are kinetically trapped metastable states. Both in toroids and rods, sliding motions are noticeable. Large toroids are generated as the intermediate conformation first, and then they become smaller through the sliding motion. © 2000 American Institute of Physics.
    The Journal of Chemical Physics 07/2000; 113(2):854-862. DOI:10.1063/1.481861 · 3.12 Impact Factor
  • Hiroshi Noguchi
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    ABSTRACT: We studied the electrophoresis of polyelectrolyte chains, such as DNA, in linear polymer solutions using Brownian dynamics simulation with anisotropic friction tensor. We show anisotropic friction is an effective method to describe dynamics of polyelectrolyte chains under an electric field in dilute polymer solution as well as in entangled polymer solution or gel. With a low anisotropy of friction, a chain fluctuates between elongated and compact states with no periodicity under a steady electric field and in field-inversion electrophoresis, its mobility shows an abrupt change at a certain chain length without antiresonance. With a high anisotropy of friction, a chain oscillates periodically and in field-inversion electrophoresis its mobility shows antiresonance. The above results agree well with experiments on DNA electrophoresis. © 2000 American Institute of Physics.
    The Journal of Chemical Physics 05/2000; 112(21):9671-9678. DOI:10.1063/1.481583 · 3.12 Impact Factor
  • K. Yoshikawa, H. Noguchi
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    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.
    Chemical Physics Letters 04/1999; 303(1-2):10-14. DOI:10.1016/S0009-2614(99)00203-1 · 1.99 Impact Factor
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    H. Noguchi, K. Yoshikawa
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    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.
    The Journal of Chemical Physics 09/1998; 109(12):5070-5077. DOI:10.1063/1.477121 · 3.12 Impact Factor
  • H. Noguchi, K. Yoshikawa
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    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.
    Chemical Physics Letters 10/1997; 278(1):184-188. DOI:10.1016/S0009-2614(97)00974-3 · 1.99 Impact Factor
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    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.
    Chemical Physics Letters 10/1996; 261(4):527-533. DOI:10.1016/0009-2614(96)00976-1 · 1.99 Impact Factor