Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

Division display 81 - 100 of about 167 ／ All the affair displays >>

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes Reviewed

Christopher M. MacDermaid, Hemant K. Kashyap, Russell H. DeVane, Wataru Shinoda, Jeffery B. Klauda, Michael L. Klein, Giacomo Fiorin

JOURNAL OF CHEMICAL PHYSICS 143 ( 24 ) 2015.12

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

The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

DOI： 10.1063/1.4937153

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

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS Reviewed

Takenobu Nakamura, Shuhei Kawamoto, Wataru Shinoda

COMPUTER PHYSICS COMMUNICATIONS 190 120 - 128 2015.5

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

An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-source molecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a spherical symmetry such as micelles and vesicles. These methods yield precise pressure fields based on the Irving-Kirkwood contour integration and are particularly useful for biomolecular force fields. The present methods are applied to several systems including a buckled membrane and a vesicle.
Program summary
Program title: Compute stress spatial
Catalogue identifier: AEVH_v1_0
Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEVH_v1_0.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 7799
No. of bytes in distributed program, including test data, etc.: 149739
Distribution format: tar.gz
Programming language: C++.
Computer: All.
Operating system: All.
Supplementary material: The input and expected output for the examples given in the manuscript can be downloaded here.
Classification: 7.7.
Nature of problem:
A precise calculation of the pressure (stress) field requires the implementation of the contour integration [2] for each pair in the cluster potentials.
Solution method:
We have implemented the method for calculating the local-volume average of the pressure field expressed by a contour integration with a delta function for the given molecular configuration obtained by molecular dynamics simulation [3].
Restrictions:
Because the definition of pressure field is based on the contour integration, the long-range interactions represented as Ewald summation are not included. In addition, the potential represented as a combination of pair and angle potential, such as Tersoff and Stillinger-Weber potential, and the interaction as a geometric constraint (shake, rigid body, etc.) are not available for current version.
Running time:
The examples provided take between 3 and 6 min each to run.
References:
[1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995) 1-19.
[2] P. Schofield and J.R. Henderson, Proc. R. Soc. Loud. A. 379 (1982) 231.
[3] T. Nakamura, W. Shinoda, and T. Ikeshoji, J. Chem. Phys. 135 (2011) 094106. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cpc.2014.11.017

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

Structures of [Li(glyme)](+) complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations Reviewed

Seiji Tsuzuki, Wataru Shinoda, Masaru Matsugami, Yasuhiro Umebayashi, Kazuhide Ueno, Toshihiko Mandai, Shiro Seki, Kaoru Dokko, Masayoshi Watanabe

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 ( 1 ) 126 - 129 2015

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

Molecular dynamics simulations of equimolar mixtures of glymes (triglyme and tetraglyme) and Li[TFSA] (lithium bis(trifluoromethylsulfonyl) amide) show that the glyme chain length affects the coordination geometries of Li+, which induces the changes in interactions between the [Li(glyme)](+) complex and [TFSA](-) anions and diffusion of ions in the equimolar mixtures.

DOI： 10.1039/c4cp04718d

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

[70]Fullerenes Assist the Formation of Phospholipid Bice Iles at Low Lipid Concentrations Reviewed

Atsushi Ikeda, Kazuya Kiguchi, Tomohiro Hida, Kazuma Yasuhara, Kazuyuki Nobusawa, Motofusa Akiyama, Wataru Shinoda

LANGMUIR 30 ( 41 ) 12315 - 12320 2014.10

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

The incorporation of neutral [70]fullerenes (C-70) led to bicelle formation in a relatively low lipid concentration range from neutral lipid mixtures (DMPC/DHPC). Furthermore, C70 addition resulted in the formation of large bicelles with a radius of ca. 100 nm, in contrast to C70-free bicelles that were formed from anionic lipid mixtures (DMPC/DHPC/DMPG). The stabilization of these bicelles was attributed to C-70 incorporation into the membranes.

DOI： 10.1021/la503732q

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

Thermodynamic Stability of [60]Fullerene and gamma-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation Reviewed

Shunsuke Mieda, Atsushi Ikeda, Yasushi Shigeri, Wataru Shinoda

JOURNAL OF PHYSICAL CHEMISTRY C 118 ( 23 ) 12555 - 12561 2014.6

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Using a supramolecular approach, water-soluble fullerenes were developed to increase the applicability of fullerenes in aqueous environments. gamma-Cyclodextrin bicapped fullerene (C-60 center dot gamma-CD) complex was proposed as one of the strong candidates to show high solubility and stability in aqueous solution. In this work, a series of free energy simulations of C-60 center dot gamma-CD complex in both water and aqueous DMSO solution has been carried out to understand the effect of solvents on the thermodynamic stability of the complex. A high stability of the complex was observed in these solvents, although the stability was slightly reduced by the addition of DMSO to aqueous solution. The reduced stability in DMSO was illuminated by the change of complex structure, as well as solvation structure. The two-dimensional free energy map for the dissociation of the C-60 center dot gamma-CD complex elucidated a possible pathway for a dissociation of single gamma-CD from the C-60 center dot gamma-CD complex. The information obtained on the molecular viewpoint might be useful to design a new stable water-soluble complex based on fullerene derivatives.

DOI： 10.1021/jp5029905

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

Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations Reviewed

Wataru Shinoda, Michael L. Klein

PURE AND APPLIED CHEMISTRY 86 ( 2 ) 215 - 222 2014.2

Language：English Publishing type：Research paper (scientific journal) Publisher：WALTER DE GRUYTER GMBH

A series of molecular dynamics (MD) simulations has been undertaken to investigate the effective interaction between vesicles including PC (phosphatidylcholine) and PE (phosphatidylethanolamine) lipids using the Shinoda-DeVane-Klein coarse-grained force field. No signatures of fusion were detected during MD simulations employing two apposed unilamellar vesicles, each composed of 1512 lipid molecules. Association free energy of the two stable vesicles depends on the lipid composition. The two PC vesicles exhibit a purely repulsive interaction with each other, whereas two PE vesicles show a free energy gain at the contact. A mixed PC/PE (1: 1) vesicle shows a higher flexibility having a lower energy barrier on the deformation, which is caused by lipid sorting within each leaflet of the membranes. With a preformed channel or stalk between proximal membranes, PE molecules contribute to stabilize the stalk. The results suggest that the lipid components forming the membrane with a negative spontaneous curvature contribute to stabilize the stalk between two vesicles in contact.

DOI： 10.1515/pac-2014-5023

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

Free energy analysis along the stalk mechanism of membrane fusion Reviewed

Shuhei Kawamoto, Wataru Shinoda

SOFT MATTER 10 ( 17 ) 3048 - 3054 2014

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

The free energy profile of the stalk model of membrane fusion has been calculated using coarse-grained molecular dynamics simulations. The proposed method guides the lipid configuration using a guiding wall potential to make the transition from two apposed membranes to a stalk and a fusion pore. The free energy profile is obtained with a thermodynamic integration scheme using the mean force working on the guiding wall as a response of the system. We applied the method to two apposed flat bilayers composed of dioleoyl phosphatidylethanolamine/dioleoyl phosphatidylcholine expanding over the simulation box under the periodic boundary conditions. The two transition states are identified as pre-stalk and pre-pore states. The free energy barrier for the latter is confirmed to be in good agreement with that estimated by the pulling method. The present method provides a practical way to calculate the free energy profile along the stalk mechanism.

DOI： 10.1039/c3sm52344f

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

Effect of different substituents on the water-solubility and stability properties of 1:2 [60]fullerene derivative·gamma-cyclodextrin complexes Reviewed

Atsushi Ikeda, Akiko Hirata, Michiko Ishikawa, Jun-Ichi Kikuchi, Shunsuke Mieda, Wataru Shinoda

Organic and Biomolecular Chemistry 11 ( 45 ) 7843 - 7851 2013.12

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

We have demonstrated that C60 derivatives bearing a pyrrolidine moiety as well as a variety of other substituents can form 1:2 complexes with γ-cyclodextrin (γ-CDx) using a mechanochemical high-speed vibration milling apparatus. When the influence of the steric hindrance of the substituents on the formation of the complexes was negligible, the water-solubilities of the complexes were shown experimentally to be completely dependent on the hydrophobic properties of the substituent. Furthermore, the stabilities of the γ-CDx-complexes of several different C60 derivatives were found to be similar to or slightly higher than that of the C60·γ-CDx complex, with the solubilities of the complexes showing no correlation to the stabilities. Based on the results of a series of theoretical investigations, we have shown that the stabilities of the γ-CDx-complexes can be affected not only by steric effects but also by the polarities of the substituent groups, which exist in the vicinity of the upper rim of γ-CDx, because the water bound to the polar group can assist in the stabilisation of the complexes. © 2013 The Royal Society of Chemistry.

DOI： 10.1039/c3ob41513a

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

Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids Reviewed

Seiji Tsuzuki, Wataru Shinoda, Md. Shah Miran, Hiroshi Kinoshita, Tomohiro Yasuda, Masayoshi Watanabe

Journal of Chemical Physics 139 ( 17 ) 2013.11

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

The stabilization energies for the formation (Eform) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G ** level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium dema and dimethylpropylammonium dmpa based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium etma based ionic liquids). The Eform for the demaCF3SO3 and dmpaCF3SO3 complexes (-95.6 and -96.4 kcal/mol, respectively) are significantly larger (more negative) than that for the etmaCF3SO3 complex (-81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl-, BF4-, TFSA - anions. The anion has contact with the N-H bond of the dema + or dmpa+ cations in the most stable geometries of the dema+ and dmpa+ complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0-18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The Eform for the less stable geometries for the dema+ and dmpa+ complexes are close to those for the most stable etma+ complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the demaTFSA and dmpaTFSA ionic liquids show that the N-H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA- anion, while the strong directionality of the interactions was not suggested from the simulation of the etma CF 3SO3 ionic liquid. © 2013 AIP Publishing LLC.

DOI： 10.1063/1.4827519

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

Intermolecular interactions in Li+-glyme and Li +-glyme-TFSA- complexes: Relationship with physicochemical properties of [Li(glyme)][TFSA] ionic liquids Reviewed

Seiji Tsuzuki, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuki Yoshida, Kaoru Dokko, Masayoshi Watanabe

ChemPhysChem 14 ( 9 ) 1993 - 2001 2013.6

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

The stabilization energies (ΔEform) calculated for the formation of the Li+ complexes with mono-, di- tri- and tetra-glyme (G1, G2, G3 and G4) at the MP2/6-311G* level were -61.0, -79.5, -95.6 and -107.7 kcal mol-1, respectively. The electrostatic and induction interactions are the major sources of the attraction in the complexes. Although the ΔEform increases by the increase of the number of the O⋯Li contact, the ΔEform per oxygen atom decreases. The negative charge on the oxygen atom that has contact with the Li+ weakens the attractive electrostatic and induction interactions of other oxygen atoms with the Li+. The binding energies calculated for the [Li(glyme)]+ complexes with TFSA- anion (glyme=G1, G2, G3, and G4) were -106.5, -93.7, -82.8, and -70.0 kcal mol-1, respectively. The binding energies for the complexes are significantly smaller than that for the Li+ with the TFSA- anion. The binding energy decreases by the increase of the glyme chain length. The weak attraction between the [Li(glyme)]+ complex (glyme=G3 and G4) and TFSA - anion is one of the causes of the fast diffusion of the [Li(glyme)]+ complex in the mixture of the glyme and the Li salt in spite of the large size of the [Li(glyme)]+ complex. The HOMO energy level of glyme in the [Li(glyme)]+ complex is significantly lower than that of isolated glyme, which shows that the interaction of the Li + with the oxygen atoms of glyme increases the oxidative stability of the glyme. The interactions in Li+-glymes-TFSA- complexes: The interactions of Li+ with glymes (tri- and tetra-glyme) are strong (-96 and -108 kcal mol-1), while the interactions of the [Li(glyme)]+ complexes with TFSA- (-82 and -70 kcal mol-1) are weaker than that between Li+ and TFSA - (-137 kcal mol-1). Copyright © 2013 WILEY-VCH Verlag GmbH &amp
Co. KGaA, Weinheim.

DOI： 10.1002/cphc.201200843

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

Regioselective recognition of a [60]fullerene-bisadduct by cyclodextrin Reviewed

Atsushi Ikeda, Michiko Ishikawa, Ryota Aono, Jun-Ichi Kikuchi, Motofusa Akiyama, Wataru Shinoda

Journal of Organic Chemistry 78 ( 6 ) 2534 - 2541 2013.3

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

The three different regioisomers of bis-N-methylfulleropyrrolidines have been separated by controlling the relative amounts of γ-cyclodextrin and dimethyl sulfoxide (DMSO) contained in solutions of these compounds. When a small amount of γ-CDx was used in a mechanochemical high-speed vibration milling apparatus, the trans-1 and trans-2•γ-CDx complexes were separated from the trans-3•γ-CDx complex. In contrast, trans-3 was extracted in a relatively high ratio with an excess of γ-CDx. The addition of DMSO to aqueous solutions of the fullerene derivative•γ-CDx complexes allowed for the three regioisomers to be obtained in high purity (&gt
95%). The basis for the observed regioselective separation was a competition between the relative stabilities and solubilities of the complexes in the water and water-DMSO solvents. The stabilities of the complexes in water were assessed by the number of hydrogen bonding interactions between the two γ-CDx units using molecular dynamics simulations. To the best of our knowledge, this is the first reported example of the isolation of the different regioisomers of fullerene derivatives using host-guest complexes. © 2013 American Chemical Society.

DOI： 10.1021/jo3027609

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

Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory Reviewed

Takenobu Nakamura, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS 138 ( 12 ) 124903 2013.3

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

A numerical method is proposed for evaluating the curvature dependency of elastic parameters of a spherical vesicle based on a calculation of the pressure profile across the membrane. The proposed method is particularly useful for small unilamellar vesicles (SUVs), in which the internal structure of the membrane is asymmetric owing to the high curvature. In this case, the elastic energy is insufficiently described as a perturbation from a planar membrane. The calculated saddle-splay curvature modulus of SUVs, which is about 16 nm in diameter, is found to be much higher than that of a planar membrane. A comparison of the free energy change in the initial stage of vesicle-to-bicelle transformation with the Fromherz theory demonstrates that the elastic parameters estimated for SUVs provide better estimation of the free energy than those estimated for a planar membrane. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4795579]

DOI： 10.1063/1.4795579

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

Computer Simulation of Self-Assembling Macromolecules Reviewed

Giacomo Fiorin, Michael L. Klein, Russell DeVane, Wataru Shinoda

HIERARCHICAL MACROMOLECULAR STRUCTURES: 60 YEARS AFTER THE STAUDINGER NOBEL PRIZE II 262 93 - 107 2013

Language：English Publishing type：Part of collection (book) Publisher：SPRINGER INT PUBLISHING AG

Amphiphilic polymers have the ability to self-assemble into supramolecular structures of great complexity and utility. Nowadays, molecular dynamics simulations can be employed to investigate the self-assembly of modestly sized natural and synthetic macromolecules into structures, such as micelles, worms ( cylindrical micelles), or vesicles composed of membrane bilayers organized as single or multilamellar structures. This article presents a perspective on the use of large-scale computer simulation studies that have been used to understand the formation of such structures and their interaction with nanoscale solutes. Advances in this domain of research have been possible due to relentless progress in computer power plus the development of so-called coarse-grained intermolecular interaction models that encode the basic architecture of the amphiphilic macromolecules of interest.

DOI： 10.1007/12_2013_262

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

Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics Reviewed

Wataru Shinoda, Dennis E. Discher, Michael L. Klein, Sharon M. Loverde

SOFT MATTER 9 ( 48 ) 11549 - 11556 2013

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

Poly(ethylene glycol) (PEG) and various zwitterionic species are now used routinely as components in soft biomaterials. The study of mixtures composed of PEGylated-lipids with zwitterionic lipids provides an excellent opportunity to understand molecular interactions in such systems. To this end, we examine the liposome/bicelle/micelle phase behavior of such mixtures in bulk solution and as monolayers at the air-water interface, utilizing a coarse-grained molecular-dynamics (CG-MD) approach rooted in experimental parameters that inform the nature of the short-range interactions. Specifically, we examine mixtures of PEGylated lipid and dimyristoylphosphatidylcholine (DMPC) lipid monolayers and find the standard force fields yield calculated surface tensions in agreement with experiment. Long-time CG-MD simulations (similar to 0.5 microsecond) of the self-assembly for different concentrations of PEG indicate the critical micellar size for the aggregate to form a bicelle from a spherical micellar nucleus. At lower PEG concentrations we find self-assembly of the PEGylated lipid into a liposome coexisting with a mixture of smaller bicelles. Examination of large individual bicelles (1000 lipids) at increasing concentrations of PEG indicates that the degree of PEG de-mixing towards the outer radius of the bicelle is correlated with the overall concentration of PEG in the bicelle. The CG-MD approach used herein should be a useful complement to experimental studies designed to probe solute (drug) interactions with such membrane systems.

DOI： 10.1039/c3sm52290c

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

A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation Reviewed

Shuhei Kawamoto, Takenobu Nakamura, Steven O. Nielsen, Wataru Shinoda

Journal of Chemical Physics 139 ( 3 ) 2013

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

A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum. © 2013 AIP Publishing LLC.

DOI： 10.1063/1.4811677

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

Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach Reviewed

Chi-cheng Chiu, Russell H. DeVane, Michael L. Klein, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

JOURNAL OF PHYSICAL CHEMISTRY C 116 ( 43 ) 23102 - 23106 2012.11

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

Functionalized single-walled carbon nanotubes (SWNTs) are widely applied in biomedical science. To understand the interaction between SWNTs and biological systems, various studies have attempted to use coarsegrained molecular dynamics (CGMD). However, there is limited validation of the existing CG models of SWNTs. Here, we present CG models for both pristine and carboxylated SVVNTs which are validated against experimental dispersion data. In addition, we present the first ever DLVO analysis of the colloidal stability of parallel SWNTs and establish that the solvent-induced repulsion between fullerenes, which is not considered in DLVO theory, is crucial to obtain a correct physical picture of SWNT dispersibility. The results presented here provide physical insight into the colloidal stability of SWNTs and can be applied to large-scale MD studies of biological systems.

DOI： 10.1021/jp307545m

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

Molecular Dynamics Study of Catanionic Bilayers Composed of Ion Pair Amphiphile with Double-Tailed Cationic Surfactant Reviewed

An-Tsung Kuo, Chien-Hsiang Chang, Wataru Shinoda

LANGMUIR 28 ( 21 ) 8156 - 8164 2012.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The physical stability of catanionic vesicles is important for the development of novel drug or DNA carriers. For investigating the mechanism by which catanionic vesicles are stabilized, molecular dynamics (MD) simulation is an attractive approach that provides microscopic structural information on the vesicular bilayer. In this study, MD simulation was applied to investigate the bilayer properties of catanionic vesicles composed of an ion pair amphiphile (IPA), hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS), and a double-tailed cationic surfactant, ditetradecyldimethylammonium chloride (DTDAC). Structural information regarding membrane elasticity and the organization and conformation of surfactant molecules was obtained based on the resulting trajectory. Simulation results showed that a proper amount of DTDAC could be used to complement the asymmetric structure between HTMA and DS, resulting in an ordered hydrocarbon chain packing within the rigid membrane observed in the mixed HTMA-DS/DTDAC system. The coexistence of gel and fluid phases was also observed in the presence of excess DTDAC. MD simulation results agreed well with results obtained from experimental studies examining mixed HTMA-DS/DTDAB vesicles.

DOI： 10.1021/la300651u

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

Computer simulation studies of self-assembling macromolecules Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

CURRENT OPINION IN STRUCTURAL BIOLOGY 22 ( 2 ) 175 - 186 2012.4

Language：English Publishing type：Research paper (scientific journal) Publisher：CURRENT BIOLOGY LTD

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.

DOI： 10.1016/j.sbi.2012.01.011

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

Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration Reviewed

David N. LeBard, Benjamin G. Levine, Russell DeVane, Wataru Shinoda, Michael L. Klein

CHEMICAL PHYSICS LETTERS 522 38 - 42 2012.1

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

Many unusual phenomena in surfactant solutions below the critical micelle concentration have been attributed to the existence of premicelles. Here we investigate the properties of premicelles in aqueous solutions of non-ionic surfactants surrounding the critical micelle concentration (CMC) using advanced computer simulations. The concentration of premicelles increases with total concentration up to the CMC, above which the concentrations of free monomers and premicelles remain nearly constant. Analysis shows premicellar structures ranging from spherical to chain-like. Monomer exchange kinetics are observed to depend strongly on the aggregate size, with premicelles exhibiting extremely short (1.3 ns) relaxation times relative to full sized micelles (72 ns). (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2011.11.075

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

Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach Reviewed

Chi-cheng Chiu, Wataru Shinoda, Russell H. DeVane, Steven O. Nielsen

SOFT MATTER 8 ( 37 ) 9610 - 9616 2012

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

The effect of carbon-based nanoparticles (CNPs) on biological systems is currently of great concern. Yet, few experimental techniques are capable of directly imaging and probing the energetics of such nano-bio systems. Here, we use coarse grain molecular dynamics simulations to study spherical fullerene molecules interacting with dipalmitoyl phosphatidylcholine (DPPC) lipid membranes. Using free energy calculations we show that all the tested fullerene molecules can spontaneously diffuse into both a lipid bilayer and a lipid monolayer. In addition, we establish that large fullerene molecules tend to partition preferentially into bilayers, which affects the lipid monolayer-to-bilayer transition during the respiration cycle. Our results identify a possible CNP perturbation to the function of the pulmonary monolayer membrane and suggest a potential pathway for CNP entry into the body through lung inhalation.

DOI： 10.1039/c2sm26357b

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

　 PREV - NEXT 　

1
2
3
4
5
6
7
8
9