Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

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A mean field approach for computing solid-liquid surface tension for nanoscale interfaces Reviewed

Chi-cheng Chiu, R. J. K. Udayana Ranatunga, David Torres Flores, D. Vladimir Perez, Preston B. Moore, Wataru Shinoda, Steven O. Nielsen

JOURNAL OF CHEMICAL PHYSICS 132 ( 5 ) 2010.2

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

The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale systems, computer simulations offer the possibility of a direct evaluation of solid-liquid surface tension although reliable methods are still under development. Here we show that using a mean field approach yields great physical insight into the calculation of surface tension and into the precise relationship between surface tension and excess solvation free energy per unit surface area for nanoscale interfaces. Previous simulation studies of nanoscale interfaces measure either excess solvation free energy or surface tension, but these two quantities are only equal for macroscopic interfaces. We model the solid as a continuum of uniform density in analogy to Hamaker's treatment of colloidal particles. As a result, the Hamiltonian of the system is imbued with parametric dependence on the size of the solid object through the integration limits for the solid-liquid interaction energy. Since the solid-liquid surface area is a function of the size of the solid, and the surface tension is the derivative of the system free energy with respect to this surface area, we obtain a simple expression for the surface tension of an interface of arbitrary shape. We illustrate our method by modeling a thin nanoribbon and a solid spherical nanoparticle. Although the calculation of solid-liquid surface tension is a demanding task, the method presented herein offers new insight into the problem, and may prove useful in opening new avenues of investigation. c 2010 American Institute of Physics. [doi: 10.1063/1.3308625]

DOI： 10.1063/1.3308625

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

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution Reviewed

Xibing He, Wataru Shinoda, Russell DeVane, Kelly L. Anderson, Michael L. Klein

CHEMICAL PHYSICS LETTERS 487 ( 1-3 ) 71 - 76 2010.2

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

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2010.01.029

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

The shear hysteresis in lamellar structure of surfactant-water binary system Reviewed

Takenobu Nakamura, Wataru Shinoda, Masuhiro Mikami

CHEMICAL PHYSICS 367 ( 1 ) 20 - 26 2010.1

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

We study the shear effect on the lamellar structure of surfactants in water using dissipative particle dynamics simulations. Starting from a lamellar structure without shear flow, we increase the shear rate and then decrease it stepwisely. A weak shear changes the lamellar plane to be parallel to the shear direction though the lamellar normal has no specific direction on the plane normal to the shear direction. By increasing the shear rate, the lamellar normal eventually flips to the vorticity direction regardless of the initial configuration. Lamellar normal would stay along the vorticity direction on decreasing the shear rate. The hysteresis is also found in shear-stress. By varying the shear rate, the time needed to reach the final unique state is significantly shortened compared with that observed with a constant shear rate. We find a correlation between the excess shear-stress and the tilt angle of surfactant in lamellar. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2009.10.009

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

Exploring the utility of coarse-grained water models for computational studies of interfacial systems Reviewed

Xibing He, Wataru Shinoda, Russell DeVane, Michael L. Klein

MOLECULAR PHYSICS 108 ( 15 ) 2007 - 2020 2010

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

Molecular dynamics simulations have become a standard tool for the investigation of biological and soft matter systems. Water models serve as the basis of force fields used in molecular dynamics simulations of these systems. This article reports on an examination of the utility of a set of coarse-grained (CG) water models, with different resolutions, interaction potentials (Lennard-Jones, Morse), and cut-off distances. The relationships between the parameters under specific choices of the above options and the thermodynamic properties, such as density, surface tension, and compressibility, were found to fit simple mathematical equations. The limits of applicability of these CG water models were explored by checking the melting temperature. If a CG site is mapped to one or two real water molecules, a simple model with appropriate combinations of cut-off distances, functional forms, and parameters can be found to simultaneously match the experimental values of density, surface tension, and compressibility under ambient conditions. If more water molecules are included in a CG site, either the melting temperature approaches or surpasses room temperature, or the surface tension and compressibility cannot both be matched simultaneously. In striving for computational efficiency, it is still possible to find a simple CG water model with three water molecules contained in a CG bead that generates a liquid state of water with realistic values of density, surface tension and compressibility at ambient condition, but coarser models are not recommended.

DOI： 10.1080/00268976.2010.503197

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

Size-dependent hydrophobic to hydrophilic transition for nanoparticles: A molecular dynamics study Reviewed

Chi-cheng Chiu, Preston B. Moore, Wataru Shinoda, Steven O. Nielsen

JOURNAL OF CHEMICAL PHYSICS 131 ( 24 ) 2009.12

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

The physical properties of nanoscale materials often vary with their size, unlike the corresponding bulk material properties, which can only be changed by modifying the material composition. In particular, it is believed that hydration phenomena are length scale dependent. The manifestation of hydrophobicity over multiple length scales plays a crucial role in self-assembly processes such as protein folding and colloidal stability. In the case of particles composed of a bulk hydrophobic material, it is well known that the free energy of hydration monotonically increases with particle size. However, the size-dependent free energy of hydration for particles composed of a bulk hydrophilic material has not been studied. Here we show that the free energy of hydration is not a monotonic function of particle size, but rather, changes sign from positive to negative as the particle size increases. In other words, the particle is hydrophobic at small size and hydrophilic at large size. This behavior arises from a purely geometrical effect caused by the curvature of the particle-water interface. We explore the consequences of this phenomenon on colloidal stability and find that it dictates the shape of colloidal aggregates.

DOI： 10.1063/1.3276915

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

Molecular Dynamics Simulations of Ionic Liquids: Cation and Anion Dependence of Self-Diffusion Coefficients of Ions Reviewed

Seiji Tsuzuki, Wataru Shinoda, Hiroaki Saito, Masuhiro Mikami, Hiroyuki Tokuda, Masayoshi Watanabe

JOURNAL OF PHYSICAL CHEMISTRY B 113 ( 31 ) 10641 - 10649 2009.8

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

Molecular dynamics simulations of a series of ionic liquids [1-alkyl-3-methylimidazolium (alkyl = methyl, ethyl, butyl, hexyl, and octyl), 1-butylpyridinium, N-butyl-N,N,N-trimethylammonium and N-butyl-N-methylpyrrolidinium cations combined with a (CF(3)SO(2))(2)N(-) anion ([mmim][TFSA], [emim][TFSA], [bmim][TFSA], [C(6)mim][TFSA], [C(8)mim][TFSA], [bpy][TFSA], [(n-C(4)H(9))(CH(3))(3)N][TFSA], and [bmpro][TFSA]) and a 1-butyl-3-methylimidazolium combined with BF(4)(-), PF(6)(-), CF(3)CO(2)(-), CF(3)SO(3)(-), and (C(2)F(5)SO(2))(2)N(-) anions ([bmim][BF(4)], [bmim][PF(6)], [bmim][CF(3)CO(2)], [bmim][CF(3)SO(3)], and [bmim][BETA])] were carried out using the OPLS force field for ionic liquids. The force field was refined on the basis of ab initio molecular orbital calculations of isolated ions and experimental densities for four ionic liquids. The densities calculated for the 13 ionic liquids agreed with the experimental values within a 2% error. The self-diffusion coefficients calculated for the ions in the 13 ionic liquids were compared with the experimental values obtained by the NMR measurements. Although the calculated self-diffusion coefficients were about 1 order smaller than the experimental ones, the cation and anion dependence (the effects of alkyl chain length in imidazolium, cation structures, and anion species) of the experimental self-diffusion coefficients was reproduced by the simulations quite well in most cases. The translational motion of the terminal carbon atoms in the alkyl chains of the imidazolium cations oil the time scale of a few nanoseconds is significantly faster than that of the atoms in the imidazolium rings and anions, which suggests that the dynamics of atoms in the polar domains of the ionic liquids is significantly different from that in the nonpolar domains. The factors determining the self-diffusion coefficients of the ions are also discussed.

DOI： 10.1021/jp811128b

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

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids Reviewed

Russell DeVane, Wataru Shinoda, Preston B. Moore, Michael L. Klein

JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5 ( 8 ) 2115 - 2124 2009.8

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

The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction performing among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parametrization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parametrized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential data set has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys 'R' Us. The model is shown to perform very well compared to other existing prediction models for these properties.

DOI： 10.1021/ct800441u

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

Models for Phosphatidylglycerol Lipids Put to a Structural Test Reviewed

Jerome Henin, Wataru Shinoda, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B 113 ( 19 ) 6958 - 6963 2009.5

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

Three atomistic empirical models for phosphatidylglycerol (PG) lipids are tested against structural data in the crystal and liquid crystal states. Simulations of the anhydrous crystal of dimyristoyl-phosphatidylglycerol (DMPG) show that only the CHARMM force field describes the conformation and interactions of PG head groups accurately. The other two models do not reproduce the native network of hydrogen bonds, suggesting the presence of biases in their conformational and nonbonded interaction properties. The CHARMM model is further validated in the biologically relevant liquid crystal phase by comparing experimental small-angle X-ray scattering spectra from DMPG unilamellar vesicles with data calculated from fluid bilayer simulations. The good agreement found in this model-free comparison implies that liquid crystal PG bilayers as described by CHARMM exhibit realistic bilayer thickness and lateral packing. Last, this model is used to simulate a fluid bilayer of palmitoyl-oleoyl-phosphatidylclycerol (POPG). The resulting view of the POPG bilayer structure is at variance with that proposed previously based on simulations, in particular, with respect to lateral packing of head groups and the role of counterions.

DOI： 10.1021/jp900645z

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

Area per Ligand as a Function of Nanoparticle Radius: A Theoretical and Computer Simulation Approach Reviewed

Robert J. B. Kalescky, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

LANGMUIR 25 ( 3 ) 1352 - 1359 2009.2

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

Inorganic nanoparticles (NPs) display unique size-dependent properties and have applications in many different areas such as medicine and the semiconductor industry. In order to take advantage of these properties, the organization of the NPs must be controlled, either to promote crystallization or to prevent agglomeration. This control is typically acheived by using covalently bound amphiphilic ligands. While the properties of the NPs themselves have been well-characterized, much less is known about the organic ligand coating. Here, we present a theoretical and computer simulation approach to compute the surface area occupied per ligand molecule as a function of the NP radius and of the ligand hydrophilic to lipophilic balance. We employ a self-consistent method which takes into account the full free energy of the NP/ligand/solvent system, which for this study is composed of hydrophobic NPs, alkyl poly(oxyethylene) ligands, and water. We find an order of magnitude higher ligand coverage on NPs compared to flat surfaces, in agreement with some experimental reports. Our approach is fundamentally different from existing computational methods in the literature and builds a foundation for studies of the organization of colloidal NPs in solvents or at interfaces.

DOI： 10.1021/la8032918

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

Fluorination effects on structure and dynamics of phospholipid bilayer: A molecular dynamics study Reviewed

Hiroaki Saito, Wataru Shinoda, Masuhiro Mikami

CHEMICAL PHYSICS LETTERS 468 ( 4-6 ) 260 - 263 2009.1

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

Comparative molecular dynamics calculations of the fluorinated and the non-fluorinated phospholipid bilayers have been carried out to examine the fluorination effects on hydration structure and lipid dynamics. The fluorination of hydrophobic chain causes an increase of hydration in the headgroup, which reorients toward the bilayer normal. Largely restricted wobbling and lateral diffusional motions were observed in the fluorinated lipid bilayer, which would be attributed to the chain stiffness of fluorinated lipids and the tight chain packing in the membrane core. The lateral diffusion coefficients obtained from these calculations show a good agreement with the experimental results. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2008.12.001

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

Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods Reviewed

Uriel Octavio Moreles Vazquez, Wataru Shinoda, Preston B. Moore, Chi-cheng Chiu, Steven O. Nielsen

JOURNAL OF MATHEMATICAL CHEMISTRY 45 ( 1 ) 161 - 174 2009.1

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

We discuss three topologically different methods for calculating the surface tension between a flat solid and a liquid from theoretical and computer simulation viewpoints. The first method, commonly used in experiments, measures the contact angle at which a static droplet of liquid rests on a solid surface. We present a new analysis algorithm for this method and explore the effects of line tension on the contact angle. The second method, commonly used computer simulations, uses the pressure tensor through the virial in a system where a thick, infinitely extended slab of liquid rests on a solid surface. The third method, which is original to this paper and is closest to the thermodynamic definition of surface tension, applies to a spherical solid in contact with liquid in which the flat solid is recovered by extrapolating the sphere radius to infinity. We find that the second and third methods agree with each other, while the first method systematically underestimates surface tension values.

DOI： 10.1007/s10910-008-9374-7

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

Computational Exploration of Novel Silicon Nanostructures Reviewed

Kengo Nishio, Taisuke Ozaki, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

ULIS 2009: 10TH INTERNATIONAL CONFERENCE ON ULTIMATE INTEGRATION OF SILICON 61 - + 2009

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

Discovery of novel Si nanostructures would open up a new avenue for science and technology as the discoveries of C-60 and carbon nanotubes did. With this expectation, we have explored novel Si nanostructures by combining empirical molecular-dynamics simulations and structure optimizations with the density functional theory(1,2,3,4). Our molecular-dynamics simulations demonstrate (1) an icosahedral Si nanodot forms by freezing a droplet in vacuum(1), (2) Si-fullerene-linked nanowires, such as Si-16- and Si-20-linked nanowires, form by freezing liquid Si inside carbon nanotubes(2), and (3) a polyicosahedral Si nanowire forms by freezing liquid Si inside a cylindrical nanopore(3). The unique cage structure of the polyicosahedral Si nanowire allows us to tune the electronic properties by encapsulating guest atoms into its cages. Our density functional theory calculations reveal that a semiconducting hydrogen-terminated polyicosahedral Si nanowire becomes metallic by the sodium and iodine doping(4).

DOI： 10.1109/ULIS.2009.4897539

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

Study on the PAN carbon-fiber-innovation for modeling a successful R&D management Reviewed

Osamu Nakamura, Tsuguyori Ohana, Masato Tazawa, Shinji Yokota, Wataru Shinoda, Junji Itoh

Synthesiology 2 ( 2 ) 154 - 164 2009

Language：English Publishing type：Research paper (scientific journal) Publisher：Nat. Inst. of Adv. Industrial Science and Technology (AIST)

We have investigated the processes of invention of PAN (Polyacrylonitrile) carbon fiber and its technology transfer to private companies. From this investigation and analysis, we have found a new R&amp
D management model, named "excited-oscillation model". This model suggests that both the top-down management and the personal motivation should be in phase and synergetic with each other. In this paper, the results and concept of the above model are described in detail.

DOI： 10.5571/syntheng.2.154

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

Enhanced hydrophobicity of fluorinated lipid bilayer: A molecular dynamics study Reviewed

Hiroaki Saito, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF PHYSICAL CHEMISTRY B 112 ( 36 ) 11305 - 11309 2008.9

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

A molecular dynamics simulation of a partially fluorinated phospholipid bilayer has been carried Out to understand the effects of fluorination of the hydrophobic chains on the structure and water permeability across the membrane. Fluorocarbon chains typically have an all-trans conformation, showing a highly ordered structure in the membrane core compared to ordinary hydrocarbon chains. The free energy profiles of water across the bilayers were successfully estimated by a revised cavity insertion Widom method. The fluorinated bilayer showed a higher free energy barrier than an ordinary nonfluorinated lipid bilayer by about 1.2 kcal/mol, suggesting a lower water permeability of the fluorinated bilayer membrane. A cavity distribution analysis elucidated the reduced free volume in the fluorinated membrane due to the neatly packed chains, which should account for the higher free energy barrier.

DOI： 10.1021/jp801057k

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

Efficient free energy calculation of water across lipid membranes Reviewed

Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF COMPUTATIONAL CHEMISTRY 29 ( 12 ) 1912 - 1918 2008.9

Language：English Publishing type：Research paper (scientific journal) Publisher：JOHN WILEY & SONS INC

An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is similar to 7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 angstrom by about 0.9 kcal/mol. (C) 2008 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.20956

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

Large-scale molecular dynamics simulations of self-assembling systems Reviewed

Michael L. Klein, Wataru Shinoda

SCIENCE 321 ( 5890 ) 798 - 800 2008.8

United-atom acyl chains for CHARMM phospholipids Reviewed

Jerome Henin, Wataru Shinoda, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B 112 ( 23 ) 7008 - 7015 2008.6

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

In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems.

DOI： 10.1021/jp800687p

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

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation Reviewed

Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS 128 ( 19 ) 2008.5

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

A statistical-mechanical treatment of the molecular binding into lipid membrane is presented in combination with molecular simulation. The membrane solution is viewed as an inhomogeneous, mixed solvent system, and the free energy of solvation of a solute in membrane is computed with a realistic set of potential functions by the method of energy representation. Carbon monoxide, carbon dioxide, benzene, and ethylbenzene are adopted as model solutes to analyze the binding into 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) membrane. It is shown that the membrane inside is more favorable than bulk water and that the solute distribution is diffuse throughout the membrane inside. The membrane-water partition coefficient is then constructed with the help of the Kirkwood-Buff theory from the solvation free energy obtained separately in the hydrophobic, glycerol, headgroup, and aqueous regions. To discuss the role of repulsive and attractive interactions, the solvation free energy is partitioned into the DMPC and water contributions and the effect of water to stabilize the benzene and ethylbenzene solutes within the membrane is pointed out. (c) 2008 American Institute of Physics.

DOI： 10.1063/1.2919117

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

Electronic and optical properties of polyicosahedral Si nanostructures: A first-principles study Reviewed

Kengo Nishio, Taisuke Ozaki, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

PHYSICAL REVIEW B 77 ( 7 ) 2008.2

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

In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has a Si-20 fullerene cage per icosahedral Si-100 nanodot. The unique cage structure is distinct from the crystalline diamond Si nanostructure. Encapsulating a guest atom into the Si-20 cage allows us to tune the electronic and optical properties. Here, we report on a systematic first-principles study of the effect of the sodium and iodine doping on the physical properties of the hydrogen-terminated polyicosahedral Si nanostructures. Our calculations reveal the strongly guest-dependent and size-dependent physical properties of the polyicosahedral Si nanostructures: (1) the semiconducting guest-free polyicosahedral nanowire becomes metallic by the sodium and iodine doping, (2) the quantum confinement effect is observed in the icosahedral and polyicosahedral nanodots, and (3) the radiative recombination rate comparable to the luminescent amorphous Si nanostructures is expected from some of the Na- and I-doped polyicosahedral nanostructures. From these results, we assert that the polyicosahedral Si nanostructures are promising candidates for the building blocks of the future nanoscale optoelectronic devices.

DOI： 10.1103/PhysRevB.77.075431

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

Coarse-grained molecular modeling of non-ionic surfactant self-assembly Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

SOFT MATTER 4 ( 12 ) 2454 - 2462 2008

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

A coarse-grained (CG) molecular model for nonionic surfactants is presented. The transferability and versatility are demonstrated by applying the model to the bulk aqueous solution as well as to the air-water and oil-water interfacial systems. The model is designed to reproduce several key properties including surface/interfacial tension, bulk density, compressibility, hydration/transfer free energy as well as distribution functions obtained by all-atom molecular dynamics simulations. The CG surfactants are demonstrated to spontaneously organize into micelles, and either hexagonal or lamellar bulk structures, respectively, at the corresponding concentration and thermodynamic conditions for those phases. Moreover, even a hexagonal-to-lamellar phase transformation is attainable using the present CG model. The experimental surface pressure-area (pi-A) curve for a representative surfactant monolayer at the air-water interface is well reproduced. Micelle budding is observed from an overly compressed monolayer; a phenomenon that is likely to be a reasonable finding because the hydration/transfer free energy is a fitted parameter in the model. The correct molecular partitioning together with a relatively rapid relaxation of the CG model system towards equilibrium enables the computation of self-assembled surfactant behavior at the mesoscale regime.

DOI： 10.1039/b808701f

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

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