Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Bec... more Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. Howev...
A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybri... more A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated-fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare submicron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.
Biochimica et Biophysica Acta (BBA) - Biomembranes
Molecular permeation through lipid membranes is a fundamental biological process that is importan... more Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Physical Review B Condensed Matter and Materials Physics, 2008
In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has... more In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has a Si20 fullerene cage per icosahedral Si100 nanodot. The unique cage structure is distinct from the crystalline diamond Si nanostructure. Encapsulating a guest atom into the Si20 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.
Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based mo... more Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C(60) interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C(60) interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C(60) lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated.
ABSTRACT The desire to model mesoscale phenomena with atomistic models places great demands on th... more ABSTRACT The desire to model mesoscale phenomena with atomistic models places great demands on the computational resources used for simulation. We recently addressed this issue by implementing the coarse grained (CG) model of Shinoda, DeVane, and Klein into the HOOMD graphical processing unit (GPU) accelerated molecular dynamics software package. The GPU implementation compares well to an optimized parallel CPU implementation running on hundreds of CPU cores. The combined efficiency of the coarse grained model and parallel performance of GPUs allows 20 GPUs to produce a microsecond of trajectory data per day for a nonionic surfactant system of 100,000 CG particles (representing approximately one million atoms). This has allowed us to calculate solution properties (e.g. critical micelle concentration) from a tremendouse data set and study dynamical processes which have been too slow to study by simulation.29-2010
ABSTRACT We studied the effects of chain branching on the water and nonionic (neutral) solute per... more ABSTRACT 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.
Langmuir the Acs Journal of Surfaces and Colloids, Feb 1, 2009
Inorganic nanoparticles (NPs) display unique size-dependent properties and have applications in m... more 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.
Molecular dynamics simulations of a series of ionic liquids [1-alkyl-3-methylimidazolium (alkyl =... more 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 on 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.
The effects of membrane curvature on the free energy barrier for membrane fusion have been invest... more The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was...
The architecture of a biological membrane hinges upon the fundamental fact that its properties ar... more 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 fiel...
ABSTRACT Nanoparticles (NPs) and surfactants can spontaneously concentrate at the interface betwe... more ABSTRACT Nanoparticles (NPs) and surfactants can spontaneously concentrate at the interface between two immiscible liquids, such as oil and water. Systems of high oil-water interfacial area, such as emulsions, are the basis of many industries and consumer products. Although NPs and surfactants are currently incorporated into many of these applications, their mutual interfacial behavior is not completely understood. Here we present molecular dynamics simulations of NPs and non-ionic surfactant in the vicinity of an oil-water interface. It was found that in low concentration the surfactants and NPs show cooperative behavior in lowering the oil-water interfacial tension, while at higher surfactant concentration this synergy is attenuated. It was also found that binding of surfactants to the NP surface decreases the surfactant efficiency in lowering the interfacial tension, while concurrently creating a barrier to NP aggregation.
In a previous molecular dynamics study, we predicted a polyicosahedral Si nanowire which has a Si... more In a previous molecular dynamics study, we predicted a polyicosahedral Si nanowire which has a Si20 fullerene cage per icosahedral Si100 nanodot [1]. The unique cage structure is distinct from the crystalline diamond Si nanowire. Encapsulating a guest atom into the Si20 cage allows us to tune the physical properties of the nanowire. Here, we report on a first-principles study of the effect of the sodium and iodine doping on the electronic band structure of the hydrogen-terminated polyicosahedral Si nanowire [2]. Our calculations reveal that the guest-free polyicosahedral Si nanowire is a semiconductor with a 1.20 eV band gap. We also find that the semiconducting nanowire becomes metallic by the sodium and iodine doping, suggesting that the electronic band structure of polyicosahedral Si nanowires can be tuned by doping appropriate guest atoms. [1] J. Chem. Phys. 125, 074712 (2006). [2] submitted to PRB
Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Bec... more Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. Howev...
A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybri... more A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated-fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare submicron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.
Biochimica et Biophysica Acta (BBA) - Biomembranes
Molecular permeation through lipid membranes is a fundamental biological process that is importan... more Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Physical Review B Condensed Matter and Materials Physics, 2008
In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has... more In a previous molecular dynamics study, we predicted a polyicosahedral Si nanostructure which has a Si20 fullerene cage per icosahedral Si100 nanodot. The unique cage structure is distinct from the crystalline diamond Si nanostructure. Encapsulating a guest atom into the Si20 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.
Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based mo... more Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C(60) interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C(60) interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C(60) lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated.
ABSTRACT The desire to model mesoscale phenomena with atomistic models places great demands on th... more ABSTRACT The desire to model mesoscale phenomena with atomistic models places great demands on the computational resources used for simulation. We recently addressed this issue by implementing the coarse grained (CG) model of Shinoda, DeVane, and Klein into the HOOMD graphical processing unit (GPU) accelerated molecular dynamics software package. The GPU implementation compares well to an optimized parallel CPU implementation running on hundreds of CPU cores. The combined efficiency of the coarse grained model and parallel performance of GPUs allows 20 GPUs to produce a microsecond of trajectory data per day for a nonionic surfactant system of 100,000 CG particles (representing approximately one million atoms). This has allowed us to calculate solution properties (e.g. critical micelle concentration) from a tremendouse data set and study dynamical processes which have been too slow to study by simulation.29-2010
ABSTRACT We studied the effects of chain branching on the water and nonionic (neutral) solute per... more ABSTRACT 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.
Langmuir the Acs Journal of Surfaces and Colloids, Feb 1, 2009
Inorganic nanoparticles (NPs) display unique size-dependent properties and have applications in m... more 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.
Molecular dynamics simulations of a series of ionic liquids [1-alkyl-3-methylimidazolium (alkyl =... more 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 on 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.
The effects of membrane curvature on the free energy barrier for membrane fusion have been invest... more The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was...
The architecture of a biological membrane hinges upon the fundamental fact that its properties ar... more 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 fiel...
ABSTRACT Nanoparticles (NPs) and surfactants can spontaneously concentrate at the interface betwe... more ABSTRACT Nanoparticles (NPs) and surfactants can spontaneously concentrate at the interface between two immiscible liquids, such as oil and water. Systems of high oil-water interfacial area, such as emulsions, are the basis of many industries and consumer products. Although NPs and surfactants are currently incorporated into many of these applications, their mutual interfacial behavior is not completely understood. Here we present molecular dynamics simulations of NPs and non-ionic surfactant in the vicinity of an oil-water interface. It was found that in low concentration the surfactants and NPs show cooperative behavior in lowering the oil-water interfacial tension, while at higher surfactant concentration this synergy is attenuated. It was also found that binding of surfactants to the NP surface decreases the surfactant efficiency in lowering the interfacial tension, while concurrently creating a barrier to NP aggregation.
In a previous molecular dynamics study, we predicted a polyicosahedral Si nanowire which has a Si... more In a previous molecular dynamics study, we predicted a polyicosahedral Si nanowire which has a Si20 fullerene cage per icosahedral Si100 nanodot [1]. The unique cage structure is distinct from the crystalline diamond Si nanowire. Encapsulating a guest atom into the Si20 cage allows us to tune the physical properties of the nanowire. Here, we report on a first-principles study of the effect of the sodium and iodine doping on the electronic band structure of the hydrogen-terminated polyicosahedral Si nanowire [2]. Our calculations reveal that the guest-free polyicosahedral Si nanowire is a semiconductor with a 1.20 eV band gap. We also find that the semiconducting nanowire becomes metallic by the sodium and iodine doping, suggesting that the electronic band structure of polyicosahedral Si nanowires can be tuned by doping appropriate guest atoms. [1] J. Chem. Phys. 125, 074712 (2006). [2] submitted to PRB
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Papers by Wataru Shinoda