Papers by noriyuki yoshii
Journal of Chemical Physics, Aug 21, 2010
Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl... more Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations
Journal of Chemical Physics, May 14, 2006
Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregate... more Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ∆G † i+j, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, Gi † , which was obtained through MD calculations. The calculated ∆G † i+j was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy 1164 Acta Physico-Chimica Sinica Vol. 34 groups and counter sodium ions on the surface of the aggregates.
International Journal of Quantum Chemistry, Dec 2, 2014
Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropr... more Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65,536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ms for a 10 million-atom system; i.e., 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.
Journal of Chemical Physics, Aug 25, 2017
We study a three-dimensional system of self-propelled Brownian particles interacting via the Lenn... more We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.
Journal of Chemical Physics, Sep 22, 1998
The Art of High Performance Computing for Computational Science, Vol. 2, 2019
In this chapter, we describe the acceleration and parallelization in classical molecular dynamics... more In this chapter, we describe the acceleration and parallelization in classical molecular dynamics simulations. As electrostatic interactions are computationally intensive, the importance of the particle mesh Ewald (PME) method and the fast multipole method (FMM) will increase. These methods will be described here. In addition, general techniques for hierarchical parallelization on the latest general-purpose supercomputers (especially connected by a three-dimensional torus network), together with the critical importance of the data array structure, are explained. We show the optimization and benchmark results in the parallel environments of the molecular dynamics calculation programs, MODYLAS and GENESIS.
The Journal of Chemical Physics, 2020
In molecular dynamics (MD) calculations of the free energies of ions and ionic molecules, we ofte... more In molecular dynamics (MD) calculations of the free energies of ions and ionic molecules, we often encounter net charged molecular systems where the electrical neutrality condition is broken. This charge causes a problem in the evaluation of long-range Coulombic interactions under periodic boundary conditions. A standard remedy for this problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of Coulombic interactions for such systems including background charge using the fast multipole method (FMM). Furthermore, an efficient scheme is developed to evaluate solute–solvent interaction energies using the FMM, reducing the computational burden for the far-field part. We calculate the hydration free energies of Mg2+, Na+, and Cl− ions dissolved in a neutral solvent using the new expression. The calculated free energies show good agreement with the results obtained using the well-estab...
THE REVIEW OF HIGH PRESSURE SCIENCE AND TECHNOLOGY, 1998
Chemical Physics Letters, 2016
Abstract In order to clarify the early-stage kinetics of micelle formation in concentrated surfac... more Abstract In order to clarify the early-stage kinetics of micelle formation in concentrated surfactant solutions, all-atom molecular dynamics (MD) calculations of the aggregation of surfactant molecules dispersed in water were performed for ionic sodium dodecyl sulfate (SDS), nonionic octaethyleneglycol monododecyl ether (C 12 E 8 ), and n -dodecane. The relationship between aggregate domain length and elapsed time from the beginning of the MD calculation obeyed the well-known Lifshitz–Slyozov (LS) law for C 12 E 8 and n -dodecane. In contrast, the aggregation rate of SDS did not obey the LS law. This difference is likely due to the differences in strength of the electrostatic interactions between the aggregates.
Molecular Simulation, 2017
We studied dynamic scaling law for the early stage domain growth in the micelle aggregation proce... more We studied dynamic scaling law for the early stage domain growth in the micelle aggregation process of dispersed surfactant molecules in water for zwitterionic dodecyldimethylamine oxide (DDAO) and cationic dodecyltrimethylammonium chloride (DTAC) based on all-atomistic molecular dynamics calculations. For both surfactants, the aggregation number N increases in proportion to t α ′, where t and α′ are the simulation time and exponent of the dynamic scaling, respectively. When the aggregation is controlled by diffusion, it follows the well-known Lifshitz-Slyozov (LS) law giving the exponent α′ = 1. The values of α′ obtained for DDAO and DTAC are 0.6 and 0.3, respectively, indicating that the aggregation rate is suppressed compared with purely diffusion controlled LS process. The aggregation of DDAO and DTAC may be partly controlled by electrostatic interaction between the aggregates.
The Journal of Chemical Physics, 2017
In our previous study, all-atomistic molecular dynamics (MD) calculations have been carried out f... more In our previous study, all-atomistic molecular dynamics (MD) calculations have been carried out for the aggregation of ionic sodium dodecyl sulfate in water [S. Kawada et al., Chem. Phys. Lett. 646, 36 (2016)]. Aggregates of 20-30 dodecyl sulfate ions were formed within a short MD run for 10 ns. However, further aggregation did not occur despite a long MD calculation for more than 100 ns. This suggests that strong electrostatic repulsive interactions between the aggregates prevent the fusion of the aggregates. In the present study, mean force and potential of mean force acting between two aggregates with aggregation number N = 30 were evaluated as a function of their separation by MD calculations. The repulsive force becomes strong with decreasing distance between the two aggregates before they merge into one. An origin of the repulsive force is an electric double layer formed by the sulfate group and counter sodium ions. Strength of the repulsive force is in good agreement with the...
membrane, 2010
A novel analytical methodology was developed by using NMR experiments and a large scale molecular... more A novel analytical methodology was developed by using NMR experiments and a large scale molecular dynamics calculation to obtain detailed information on thermodynamic stability, mobility, and kinetics of binding/dissociation of drugs in lipid membranes and micelles. First, the drug binding and mobility in lipid bilayer membrane were quantified in situ by using the multinuclear solution NMR combined with the pulsed-field-gradient (PFG) technique. One-dimensional and PFG 19 F and 1 H NMR signals of an anticancer drug, 5-fluorouracil (5FU) were analyzed in the presence of large unilamellar vesicles (LUVs) of egg phosphatidylcholine (EPC) as model cell membranes. The simultaneous observation of the membrane-bound and free 5FU signals enables to quantify in what amount of 5FU is bound to the membrane and how fast 5FU is moving within the membrane. The kinetics of membrane binding and dissociation was also quantified by PFG NMR. The 19 F NMR signal of 5FU was analyzed by the solution of Bloch equation with exchange terms. The rate constants of 5FU binding and dissociation were determined and compared with the translational diffusion. Finally, the stability of a water molecule in the core of the micelle was investigated quantitatively from calculating the free energy of transfer from the bulk to micelle core, by using the thermodynamic integration method based on a molecular dynamics calculation.
THE REVIEW OF HIGH PRESSURE SCIENCE AND TECHNOLOGY, 2000
Journal of Chemical Theory and Computation, 2013
Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropr... more Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65,536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ms for a 10 million-atom system; i.e., 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.
The Journal of Chemical Physics, 1998
A series of molecular dynamics calculations for water has been carried out along an isochore at 1... more A series of molecular dynamics calculations for water has been carried out along an isochore at 1 g/cm3 and an isotherm at 600 K in order to examine microscopic properties of water in the sub- and supercritical states. A polarizable potential model proposed by Dang (RPOL model) was employed to take into account the state dependence of intermolecular interaction. Along the isochore, fluid structure changes from tetrahedral icelike structure at room temperature to simple-liquidlike one at high temperatures. Orientational correlation between a tagged molecule and its neighbors is reduced substantially with increasing temperature, though hydrogen bonds between two molecules persist even at 600 K. As temperature increases, the number of the hydrogen bonds per molecule decreases monotonically from 3.2 at 280 K to 1.9 at 600 K. The activation barrier for diffusion at 600 K is about half as large as that at room temperature. A collective polarization relaxation loses collective character ab...
The Journal of Chemical Physics, 2007
In our previous analysis of the structural stability of a sodium dodecyl sulfate (SDS) micelle ba... more In our previous analysis of the structural stability of a sodium dodecyl sulfate (SDS) micelle based on molecular dynamics calculation, vacancies were found in the center of the micelles [N. Yoshii and S. Okazaki, Chem. Phys. Lett.425, 58 (2006)]. It is very interesting to clarify whether a water molecule is expected in the vacancy in thermodynamic equilibrium at room temperature. In order to investigate the stability of water in the core of micelle, free energy of transfer of water from bulk to the core has been calculated for the SDS micelle in water for two micelle sizes, N=61 and 121, at temperature T=300 K and pressure P=1 atm. The calculated free energy of transfer, ΔGc←b, from the bulk to the core is about 28±4 kJ∕mol and 26±4 kJ∕mol for the micelle of the size N=61 and 121, respectively, where the corresponding Boltzmann factor, exp(−ΔGc←b∕kT), is in the order of one over several ten thousands. Thus, a water molecule hardly permeates into the core of the micelle.
The Journal of Chemical Physics, 2006
Free energy of micelle formation has been evaluated for spherical sodium dodecyl sulfate (SDS) in... more Free energy of micelle formation has been evaluated for spherical sodium dodecyl sulfate (SDS) in water by a thermodynamic integration method combined with a series of large-scale molecular dynamics calculations following the chemical species model. In particular, free energy change Δμn+10 with respect to the addition of one surfactant molecule to the spherical micelle of size n was obtained as a function of n. The free energy profile showed a minimum followed by a maximum, which corresponds to a peak in the size distribution. The calculated peak size n=57 near its critical micelle concentration is in good agreement with the experimental averaged aggregation number n=55–75 of the SDS micelle. The distribution showed a rather sharp peak, indicating that the size is almost a monodisperse one. The size is likely to be insensitive to the total concentration of the surfactant.
The Journal of Chemical Physics, 1997
A number of large-scale and long-time molecular dynamics calculations, N=10 976 and t=1 ns, have ... more A number of large-scale and long-time molecular dynamics calculations, N=10 976 and t=1 ns, have been performed for the supercritical Lennard-Jones fluid at various densities along an isotherm at T=1.03Tc in order to investigate the structure and dynamics of clusters formed in the fluid as well as the fluid itself. The calculations successfully demonstrated both Ornstein–Zernike behavior of structure factor at small k region and critical slowing down in dynamic structure factor near the critical density. A molecular based picture for these phenomena in real space has been presented by newly defining several statistical mechanical correlation functions and distribution functions. A few static and dynamic properties of clusters such as generation and annihilation dynamics and single particle and collective energy fluctuations are also given.
The Journal of Chemical Physics, 2010
Free energy of transfer, ΔGw→m, from water phase to a sodium dodecyl sulfate (SDS) micelle core h... more Free energy of transfer, ΔGw→m, from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated ΔGw→m’s are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol−1 per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively.
The Journal of Chemical Physics, 2012
The free energy profiles, ΔG(r), for penetration of methane and water molecules into sodium dodec... more The free energy profiles, ΔG(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6–12 kJ mol−1 more stable in the SDS micelle than in the water phase, and no ΔG(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to ΔG(r), it is clear that methane in the SDS micelle is about 25 kJ mol−1 more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5–15 kJ mol−1 by the contribution from...
Uploads
Papers by noriyuki yoshii