An exa-scale high-performance molecular dynamics simulation program: MODYLAS.

A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization.

Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations.

In the era of exascale supercomputers, large-scale, and long-time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)-communication in the MPI-parallelized fast multipole method (FMM) combined with MD calculations under three-dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM.

Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation.

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.

Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure.

The fast multipole method (FMM) is an order N method for the numerically rigorous calculation of the electrostatic interactions among point charges in a system of interest. The FMM is utilized for massively parallelized software for molecular dynamics (MD) calculations. However, an inconvenient limitation is imposed on the implementation of the FMM: In three-dimensional case, a cubic MD unit cell is hierarchically divided by the octree partitioning under isotropic periodic boundary conditions along three axes.

Fast multipole method for three-dimensional systems with periodic boundary condition in two directions.

We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector.

Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether.

Molecular dynamics calculations of a mixed micelle composed of sodium dodecyl sulfate (SDS) and octaethylene glycol monododecyl ether (C E ) were performed for six compositions (SDS/C E = 100/0, 80/20, 60/40, 40/60, 20/80, and 0/100) to investigate the composition dependence of the mixed micelle structure and solubilization of cyclohexane, benzene, and phenol molecules by the micelle. The radial density distribution of the hydrophilic polyoxyethylene (POE) group of C E as a function of distance from the micelle center is very sharp for micelles with high SDS content because the POE group captures a Na ion in solution and wraps around it to form a compact crown-ether-like complex. The hydrophobic dodecyl groups of SDS and C E were separately distributed in the mixed micelle core.

Pressure tensor for electrostatic interaction calculated by fast multipole method with periodic boundary condition.

A microscopic expression of the pressure tensor using the fast multipole method (FMM) with periodic boundary conditions has been derived. The pressure tensor calculated using this expression has been compared with that obtained using the Ewald method with high accuracy. The precision of the pressure tensor can be controlled as a function of expansion order p of FMM.

Molecular dynamics study of the potential of mean force of SDS aggregates.

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.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic CE micelles: A molecular dynamics study.

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (CE) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor.

Evaluation of atomic pressure in the multiple time-step integration algorithm.

In molecular dynamics (MD) calculations, reduction in calculation time per MD loop is essential. A multiple time-step (MTS) integration algorithm, the RESPA (Tuckerman and Berne, J. Chem.

A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water.

To obtain the radial (normal) and lateral (transverse) components of the local pressure tensor, PN(R) and PT(R), respectively, and the interfacial tension of micelles, molecular dynamics (MD) calculations were performed for spherical sodium dodecyl sulfate (SDS) micelles. The local pressure tensor was calculated as a function of radial distance R using the Irving-Kirkwood formula. Similar MD calculations were also carried out for an n-dodecane droplet in water to compare the differences in the local pressure and interfacial tension values with those of the micelles.

A molecular dynamics study of the breathing and deforming modes of the spherical ionic SDS and nonionic C12E8 micelles.

In order to investigate shape of the micelles and its thermal fluctuations, molecular dynamics calculations have been performed for spherical ionic sodium dodecyl sulfate (SDS) and nonionic octaethyleneglycol monododecyl ether (C12E8) micelles. New statistical functions suitable for extracting the fluctuations of the shape of the spherical micelles were defined using spherical harmonics and Legendre polynomials. The breathing and deforming modes of the SDS and C12E8 micelles were analyzed in detail based on these new functions.

MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms.

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).

Lateral diffusion of lipids separated from rotational and translational diffusion of a fluid large unilamellar vesicle.

A new method to separate lateral diffusion of lipids in spherical large unilamellar vesicles from the rotational and the translational diffusion of the vesicle as a whole is proposed. The lateral diffusion coefficient DL is obtained as a time-dependent part of the observed diffusion coefficient in vesicles of 800-nm diameters, by systematically changing the diffusion time interval of the high-field-gradient NMR measurement. Although the lipid is in a confined space, the DL of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine is (1.

Kinetics of binding and diffusivity of leucine-enkephalin in large unilamellar vesicle by pulsed-field-gradient H NMR .

The kinetics of binding, the diffusivity, and the binding amount of a neuropeptide, leucine-enkephalin (L-Enk) to lipid bilayer membranes are quantified by pulsed-field-gradient (PFG) H NMR . The peptide signal is analyzed by the solution of the Bloch equation with exchange terms in the presence of large unilamellar vesicles (LUVs) as confined, but fluid model cell membranes. Even in the case that the membrane-bound and the free states of L-Enk cannot be distinguished in the one-dimensional NMR spectrum, the PFG technique unveils the bound component of L-Enk after the preferential decay of the free component at the high field gradient.

Binding of hydrophobic fluorinated bisphenol A to large unilamellar vesicles of egg phosphatidylcholine.

The kinetics of membrane binding and dissociation of fluorinated bisphenol A (FBPA, (CF(3))(2)C(C(6)H(4)OH)(2)) is quantified by 1D (19)F NMR spectra in situ. Although the bound and free components are in fast exchange, the rate constants and bound fraction is nonetheless determined from an analysis of the spectra. The analysis relies on the expression of 1D NMR signal intensity by a set of Bloch equations with exchange terms.

All-atom molecular dynamics study of a spherical micelle composed of N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) block copolymers: a potential carrier of drug delivery systems for cancer.

An all-atom molecular dynamics simulation of a spherical micelle composed of amphiphilic N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) (PEG-PBLG-Ac) block copolymers was performed in aqueous solution at 298.15 K and 1 atm. Such copolymers have received considerable attention as carriers in drug delivery systems.

Drug binding and mobility relating to the thermal fluctuation in fluid lipid membranes.

Drug binding and mobility in fluid lipid bilayer membranes are quantified in situ by using the multinuclear solution NMR combined with the pulsed-field-gradient technique. One-dimensional and pulsed-field-gradient (19)F and (1)H NMR signals of an anticancer drug, 5-fluorouracil (5FU) are analyzed at 283-313 K 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 in relation to the thermal fluctuation of the soft, fluid environment.

A molecular dynamics study of free energy of micelle formation for sodium dodecyl sulfate in water and its size distribution.

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 delta mu(n+1)0 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.