Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

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Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants Reviewed

W. Shinoda, R. Devane, M. L. Klein

MOLECULAR SIMULATION 33 ( 1-2 ) 27 - 36 2007.1

Language：English Publishing type：Research paper (scientific journal) Publisher：TAYLOR & FRANCIS LTD

A new systematic approach to build coarse-grained (CG) molecular models for surfactants/water systems is proposed. A step-by-step approach using several molecular systems for the parameterization makes the CG model versatile and transferable. The intramolecular bond potentials are determined to reproduce the bond and angle distributions obtained from all-atom (AA) molecular dynamics (MD) simulations. A careful choice of the potential function for nonbonded interactions is essential for better structural properties. Density and surface/interfacial tension data are used for parameter fitting, because these thermodynamic properties are of key importance in characterizing the self-organized surfactant structure. Solvation (hydration) and transfer free energies, which play an essential role in determining the partition of solute molecules, are also taken into account in the model.

DOI： 10.1080/08927020601054050

Other Link： http://orcid.org/0000-0002-3388-9227

Molecular dynamics simulation of an archaeal lipid bilayer with sodium chloride Reviewed

Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 9 ( 5 ) 643 - 650 2007

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

We have performed molecular dynamics simulations of a bilayer formed by the synthetic archaeal lipid, diphytanyl phosphatidylcholine, in NaCl electrolyte solution at four different concentrations (0-4 M) to investigate how structural and dynamic properties of the model archaeal membrane are changed due to the ionic strength of the solution. The archaeal lipid bilayer shows minor changes in their physical properties, indicating the unusual high stability of the membrane against salt, though small reductions of molecular area and lateral diffusion of the lipid are detected at the highest electrolyte concentration of 4 M. Sodium ions penetrate to the ether-rich region, where the ions are likely bound to the ether oxygen in the sn-1 chain rather than to that in the sn-2 chain. The observed salt bridges among two or three neighboring lipids account for the small reduction in the molecular area. The bound ions together with the counter ( chloride) ions give rise to a diffusive electric double layer; as a result, the membrane dipole potential is slightly increased with increasing NaCl concentration.

DOI： 10.1039/b611543h

Other Link： http://orcid.org/0000-0002-3388-9227

Molecular dynamics study of bipolar tetraether lipid membranes Reviewed

W Shinoda, K Shinoda, T Baba, M Mikami

BIOPHYSICAL JOURNAL 89 ( 5 ) 3195 - 3202 2005.11

Language：English Publishing type：Research paper (scientific journal) Publisher：BIOPHYSICAL SOCIETY

Membranes composed of bipolar tetraether lipids have been studied by a series of 25-ns molecular dynamics simulations to understand the microscopic structure and dynamics as well as membrane area elasticity. By comparing macrocyclic and acyclic tetraether and diether archaeal lipids, the effect of tail linkage of the two phytanyl-chained lipids on the membrane properties is elucidated. Tetraether lipids show smaller molecular area and lateral mobility. For the latter, calculated diffusion coefficients are indeed one order-of-magnitude smaller than that of the diether lipid. These two tetraether membranes are alike in many physical properties except for membrane area elasticity. The macrocyclic tetraether membrane shows a higher elastic area expansion modulus than its acyclic counterpart by a factor of three. Free energy profiles of a water molecule crossing the membranes show no major difference in barrier height; however, a significant difference is observed near the membrane center due to the lack of the slip-plane in tetraether membranes.

DOI： 10.1529/biophysj.105.060962

Calculation of heat capacities of light and heavy water by path-integral molecular dynamics Reviewed

Motoyuki Shiga, Wataru Shinoda

Journal of Chemical Physics 123 ( 13 ) 134502 2005.10

Language：English Publishing type：Research paper (scientific journal)

As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2 O at 300 K, 6.9 in the liquid H2 O at 300 K, and 4.1 in the ice Ih H2 O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2 O has been calculated to be 10% higher than that of H2 O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions. © 2005 American Institute of Physics.

DOI： 10.1063/1.2035078

Quantum simulation of the heat capacity of water Reviewed

Wataru Shinoda, Motoyuki Shiga

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 71 ( 4 ) 2005.4

Language：English Publishing type：Research paper (scientific journal)

Path integral molecular dynamics simulations have been carried out to evaluate heat capacities of water in gas, liquid, and solid phases. For convergence, a 100-ps simulation run with a large path integral variable (P ∼ 128) was required even by using the double-centroid virial heat capacity estimator. For all states, the quantum corrections to the heat capacities are significantly large. The calculated heat capacities for vapor and ice I h agreed excellently with experimental data, while that for liquid was less than the experimental value by ∼20% due to the limit of the SPC/F potential model. © 2005 The American Physical Society.

DOI： 10.1103/PhysRevE.71.041204

Spatial confinement effect on the atomic structure of solid argon Reviewed

K Nishio, W Shinoda, T Morishita, M Mikami

JOURNAL OF CHEMICAL PHYSICS 122 ( 12 ) 2005.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER INST PHYSICS

Molecules confined in nanopores show unusual behavior not seen in bulk systems. The present paper reports on molecular dynamics simulations of unusual freezing behavior in confined Ar. Similar to bulk Ar, liquid Ar confined in pores with a diameter D>15 sigma (5.1 nm), where sigma is the diameter of the Ar atom, crystallizes when the cooling rate is lower than a critical value (Q(c)). We also find that the spatial confinement does not have significant influence on Q(c) when D>15 sigma (5.1 nm). In the pore of 10 sigma (3.4 nm) in diameter, on the other hand, the behavior is dramatically changed. Crystalline Ar does not appear inside the pore even when the system is cooled at a rate lower than the Q(c) in the bulk system by over two orders of magnitude. Instead, amorphous Ar characterized by local icosahedral configurations is formed in the pore. We further find that, even when crystalline Ar is formed outside the pore, it does not grow deeply into the pore. This supports that the amorphous Ar is actually the most stable phase in the pore. It is well known that Ar is a poor glass former. Our finding that even such an amorphous Ar is the most stable in the pore suggests that, in any system, it is possible to prepare amorphous structure selectively by using nano-molds.

DOI： 10.1063/1.1878693

Other Link： http://orcid.org/0000-0002-3388-9227

Can such long time steps really be used in dissipative particle dynamics simulations? Reviewed

B Hafskjold, CC Liew, W Shinoda

MOLECULAR SIMULATION 30 ( 13-15 ) 879 - 885 2004.11

Language：English Publishing type：Research paper (scientific journal) Publisher：TAYLOR & FRANCIS LTD

Commonly used time steps in dissipative particle dynamics (DPD) simulations are too large and lead to systematic errors in the computed properties. The main source of errors is the inaccurate integration of the conservative force. This error can be reduced to some extent by constructing a smoother force without any abrupt change at the cut-off distance, but the improvement is marginal. Alternatively, we tried smooth forces that also lead to the same conclusion. It is possible to find combinations of parameters for the random and dissipative forces that make errors cancel, but the combinations will depend on the system's thermodynamic state and on the particular force model. The only safe procedure is to use small time steps, i.e. comparable with those used in MD simulations. Alternatively, an improved integration algorithm should be used for the conservative force.

DOI： 10.1080/08927020410001709370

Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers Reviewed

K Shinoda, W Shinoda, T Baba, M Mikami

JOURNAL OF CHEMICAL PHYSICS 121 ( 19 ) 9648 - 9654 2004.11

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER INST PHYSICS

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data. (C) 2004 American Institute of Physics.

DOI： 10.1063/1.1806791

Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study Reviewed

M Shiga, W Shinoda

PHYSICAL REVIEW B 70 ( 5 ) 054102 2004.8

Language：English Publishing type：Research paper (scientific journal) Publisher：AMERICAN PHYSICAL SOC

The sliding in a Ni symmetrical tilt grain boundary, Sigma5 (012) [100], is investigated by modified Parrinello-Rahman molecular dynamics which deals with the thermodynamic ensemble characterized by the number of atoms N, temperature T, and the shear stress t. It is found that the grain boundary can slide in the direction perpendicular to the tilt axis [02(1) over bar] with the aid of shear stress in that direction. The sliding is coupled to the migration involving a collective motion of the third layer atoms hopping into the hollow site in between the first (GB) and second layers. Here, the critical stress necessary to move the grain boundary damps almost exponentially as the temperature is increased. At temperatures above about 820 K, random walk of GB migration occurs without the assistance of stress. On the other hand, it is only at much higher shear stress that the grain boundary can slide in the direction parallel to the tilt axis [001]. This may be because this sliding mechanism does not involve the coupling to the migration mode.

DOI： 10.1103/PhysRevB.70.054102

Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers: 2. Permeability Reviewed

W Shinoda, M Mikami, T Baba, M Hato

JOURNAL OF PHYSICAL CHEMISTRY B 108 ( 26 ) 9346 - 9356 2004.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We studied the effects of chain branching on the water and nonionic (neutral) solute permeability of lipid bilayers in a molecular dynamics simulation comparing two bilayers: dipalmitoylphosphatidylcholine (DPPC) and diphytanoylphosphatidylcholine (DPhPC). The calculated free energy profiles of several neutral solute and water molecules across the lipid membranes showed that chain branching caused no significant changes in the solubility of these molecules inside the membrane core. However, an analysis of the cavity distribution in each of these bilayer systems demonstrated that the branch-chained DPhPC bilayer had, compared with the straight-chained DPPC bilayer, a relatively small and discrete free volume distribution in the hydrophobic part. This suggests that small penetrants have a lower rate of diffusion inside branch-chained lipid bilayers. Actually, water molecules showed lower local diffusion coefficients inside the DPhPC membrane than inside the DPPC membrane. The low penetrant mobility of the former must correlate with the slower dynamics of the branched DPhPC chains. Thus, we conclude that chain branching effects on the permeability are, as far as neutral small penetrants are concerned, attributable mainly to the reduction of chain dynamics. The effects of chain branching on proton permeability are also discussed in the context of the proton-wire hypothesis.

DOI： 10.1021/jp035998+

Two-dimensional self-assembled structures of adenine molecules: modeling and simulation Reviewed

K Shinoda, W Shinoda, CC Liew, S Tsuzuki, Y Morikawa, M Mikami

SURFACE SCIENCE 556 ( 2-3 ) 109 - 120 2004.5

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Self-assembly of adenine molecules deposited on a Cu(1 1 1) surface shows some characteristic hydrogen-bonding network patterns, such as hexagonal and 'double-chain'. In order to understand the emergence of energetically less favorable 'double-chain' structure, in which adenine molecules form two rows, possible molecular arrangements in the 'double-chain' structure are investigated by potential energy surface (PES) calculations between two single chains. A series of PES calculations elucidates that there are various stable molecular arrangements for the chain pair models: some of the models have both hexagonal and 'double-chain' (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained 'double-chain' structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type 'double-chain' structures remain even at 300 K, while all I-type ones transform into hexagonal arrays. The former result reminds us that the II-type 'double-chain' structures should be observed at room temperature in the STM experiment. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.susc.2004.03.022

Dynamics of a highly branched lipid bilayer: a molecular dynamics study Reviewed

W Shinoda, M Mikami, T Baba, M Hato

CHEMICAL PHYSICS LETTERS 390 ( 1-3 ) 35 - 40 2004.5

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

A comparison of branch-chained diphytanoylphosphatidylcholine (DPhPC) and straight-chained dipalmitoylphosphatidylcholine (DPPC) for their dynamics in the bilayers is made using 10 ns molecular dynamics simulations in the microcanonical ensemble. It is demonstrated that DPhPC molecules, compared with DPPC, indeed have slower wobbling, rotational, and translational motions by a factor of 2-3, whereas slightly faster headgroup rotation. The revision of the lipid dynamics due to chain branching is similar to that observed by the addition of cholesterol. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2004.03.145

Rapid estimation of elastic constants by molecular dynamics simulation under constant stress Reviewed

W Shinoda, M Shiga, M Mikami

PHYSICAL REVIEW B 69 ( 13 ) 134103 2004.4

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC

Molecular simulations, when they are used to understand properties characterizing the mechanical strength of solid materials, such as stress-strain relation or Born stability criterion, by using elastic constants, are sometimes seriously time consuming. In order to resolve this problem, we propose an efficient simulation approach under constant external stress and temperature, modifying Parrinello-Rahman (PR) method using useful sampling techniques developed recently-massive Nose-Hoover chain method and hybrid Monte Carlo method. Test calculations on the Ni crystal employing the embedded atom method have shown that our method greatly improved the efficiency in sampling the elastic properties compared with the conventional PR method.

DOI： 10.1103/PhysRevB.69.134103

Molecular dynamics study of the lipid bilayers: Effects of the chain branching on the structure and dynamics Reviewed

W Shinoda, M Mikami, T Baba, M Hato

SLOW DYNAMICS IN COMPLEX SYSTEMS 708 352 - 353 2004

Language：English Publishing type：Research paper (international conference proceedings) Publisher：AMER INST PHYSICS

We studied effects of lipid chain branching on structural and dynamical properties of the lipid bilayers by a comparative molecular dynamics simulation of dipalmitoyl phosphatidylcholine (DPPC) and diphytanoyl phosphatidylcholine (DPhPC) bilayers. Trans-gauche isomerization rate at the dihedrals along the hydrophobic main chain was significantly reduced by chain branching. The slower conformational motion of branched chains lead to slower wobbling of the chain and slower rotational and translational motions of the lipid molecules, compared with straight-chained counterpart. In contrast. headgroup motion was slightly enhanced by the chain branching. The slower dynamics of the branched hydrophobic chains accounts for the high structural bilayer stability and low solute permeability of the branched DPhPC bilayer.

DOI： 10.1063/1.1764171

Other Link： http://orcid.org/0000-0002-3388-9227

1P108 MD Simulation of Halorhodopsin in Lipid bilayer

Hayashi M., Miyagawa Y., Shinoda W., Sakurai M.

Seibutsu Butsuri 44 S56 2004

Molecular dynamics study on the effect of chain branching on the physical properties of lipid bilayers: Structural stability Reviewed

W Shinoda, M Mikami, T Baba, M Hato

JOURNAL OF PHYSICAL CHEMISTRY B 107 ( 50 ) 14030 - 14035 2003.12

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

In general, bilayers composed of branch-chained lipid molecules are known to have high stability and low ion permeability. To understand how chain branching affects bilayer properties on a molecular level, two molecular dynamics (MD) simulations of lipid bilayers have been undertaken in the isothermal-isobaric ensemble. The first MD simulation was carried out on the straight-chained DPPC bilayer, and the second was carried out on the branch-chained DPhPC bilayer. Chain branching reduced segmental order of the lipid chain. This would be closely related to a high gauche probability at the dihedrals in the vicinity of tert-carbons; these dihedrals brought about the chain bending at the branched segments. Due to the characteristic conformation of the branched chain, some different effects were observed: First, the probability of parallel orientation of the two chains in a lipid was reduced; second, a chain caught between the two chains of the neighboring lipid in the same leaflet of the bilayer was frequently observed. As a consequence, the branched chain showed a much lower overall rate of trans-gauche isomerization than its straight counterpart. In conclusion, the high structural stability of the branched DPhPC bilayer is attributable mainly to the slow conformational motion of the hydrophobic chain, which is clearly correlated with the observed chain "entrapment" between the lateral neighboring lipid molecules.

DOI： 10.1021/jp035493j

Other Link： http://orcid.org/0000-0002-3388-9227

A comparison of straight- and branch-chained lipid bilayers for static and dynamic properties: A molecular dynamics study Reviewed

W Shinoda, M Mikami, T Baba, M Hato

NANOTECH 2003, VOL 3 3 512 - 515 2003

Language：English Publishing type：Research paper (international conference proceedings) Publisher：COMPUTATIONAL PUBLICATIONS

A bilayer composed of branch-chained lipid molecules is generally believed to have high bilayer stability and low ion leakage. To understand how the chain branching affects the bilayer properties on the molecular level, two molecular dynamics simulations of lipid bilayers have been undertaken in the isothermal-isobaric ensemble. The first simulation was carried out on the straight-chained DPPC bilayer, the second on the branch-chained DPhPC. The detailed analyses on the chain conformation revealed that the segmental order of branched chains was lower than that of straight chains. As for the intermolecular packing order in the bilayer plane, however, a relatively neat lipid arrangement was observed for the branch-chained DPhPC bilayer. A significant lowering in the chain mobility was observed as a result of chain branching. The high bilayer stability of the branch-chained DPhPC bilayer would arise from the low chain mobility and the neat lateral arrangement of the lipid in the bilayer.

Other Link： http://orcid.org/0000-0002-3388-9227

1G0930 A comparison of straight- and branch-chained lipid bilayers for the static and dynamic properties a molecular dynamics study.

Shinoda W., Mikami M., Baba T., Hato M.

Seibutsu Butsuri 42 ( 2 ) S35 2002

Self-guided molecular dynamics in the isothermal-isobaric ensemble Reviewed

W Shinoda, M Mikami

CHEMICAL PHYSICS LETTERS 335 ( 3-4 ) 265 - 272 2001.2

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

The self-guided molecular dynamics (SGMD) method, which was proposed recently to enhance the efficiency of conformational sampling, has been extended to the isothermal-isobaric ensemble. It was applied to the crystallization of argon fluid in a supercooled state, and verified that crystallization was considerably accelerated with a suitable parameter set for the SGMD method. The algorithm proposed here also works well in the case of pressure-induced crystallization. A series of examinations we have done elucidates the applicable targets that SGMD works effectively. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(01)00054-9

Other Link： http://orcid.org/0000-0002-3388-9227

Molecular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: An effect of the potential force fields on the membrane structure. Reviewed

W Shinoda, S Okazaki

JOURNAL OF MOLECULAR LIQUIDS 90 ( 1-3 ) 95 - 103 2001.2

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

In order to obtain a better description for the membrane area of a lipid bilayer, the potential parameter set OPLS, modified with respect to the interaction for the alkyl chain, was adopted for the present molecular dynamics simulation. A long-time and large-scale calculation based upon this modified potential presented a remarkable improvement of the membrane area for the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase, showing a good agreement with experiment. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0167-7322(01)00111-8

Other Link： http://orcid.org/0000-0002-3388-9227

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