Yoshimichi Andoh

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). 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; that is, 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.

Effect of bubble formation on the dissociation of methane hydrate in water: a molecular dynamics study.

We investigate the dissociation of methane hydrate in liquid water using molecular dynamics simulations. As dissociation of the hydrate proceeds, methane molecules are released into the aqueous phase and eventually they form bubbles. It is shown that this bubble formation, which causes change in the methane concentration in the aqueous phase, significantly affects the dissociation kinetics of methane hydrate. A large system size employed in this study makes it possible to analyze the effects of the change in the methane concentration and the formation of bubbles on the dissociation kinetics in detail. It is found that the dissociation rate decreases with time until the bubble formation and then it turns to increase. It is also demonstrated that methane hydrate can exist as a metastable superheated solid if there exists no bubble.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution.

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10(6) all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200,000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsids tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Dissociation of methane hydrate in aqueous NaCl solutions.

Molecular dynamics simulations of the dissociation of methane hydrate in aqueous NaCl solutions are performed. It is shown that the dissociation of the hydrate is accelerated by the formation of methane bubbles both in NaCl solutions and in pure water. We find two significant effects on the kinetics of the hydrate dissociation by NaCl. One is slowing down in an early stage before bubble formation, and another is swift bubble formation that enhances the dissociation. These effects arise from the low solubility of methane in NaCl solution, which gives rise to a nonuniform spatial distribution of solvated methane in the aqueous phase. We also demonstrate that bubbles form near the hydrate interface in dense NaCl solutions and that the hydrate dissociation proceeds inhomogeneously due to the bubbles.

Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells

Molecular dynamics (MD) calculations for the plasma membranes of normal murine thymocytes and thymus-derived leukemic GRSL cells in water have been performed under physiological isothermal-isobaric conditions (310.15K and 1 atm) to investigate changes in membrane properties induced by canceration. The model membranes used in our calculations for normal and leukemic thymocytes comprised 23 and 25 kinds of lipids, respectively, including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. The mole fractions of the lipids adopted here were based on previously published experimental values. Our calculations clearly showed that the membrane area was increased in leukemic cells, and that the isothermal area compressibility of the leukemic plasma membranes was double that of normal cells. The calculated membranes of leukemic cells were thus considerably bulkier and softer in the lateral direction compared with those of normal cells. The tilt angle of the cholesterol and the conformation of the phospholipid fatty acid tails both showed a lower level of order in leukemic cell membranes compared with normal cell membranes. The lateral radial distribution function of the lipids also showed a more disordered structure in leukemic cell membranes than in normal cell membranes. These observations all show that, for the present thymocytes, the lateral structure of the membrane is considerably disordered by canceration. Furthermore, the calculated lateral self-diffusion coefficient of the lipid molecules in leukemic cell membranes was almost double that in normal cell membranes. The calculated rotational and wobbling autocorrelation functions also indicated that the molecular motion of the lipids was enhanced in leukemic cell membranes. Thus, here we have demonstrated that the membranes of thymocyte leukemic cells are more disordered and more fluid than normal cell membranes.

A molecular dynamics study of the lateral free energy profile of a pair of cholesterol molecules as a function of their distance in phospholipid bilayers

Free energy profile of a pair of cholesterol molecules in a leaflet of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayers in the liquid-crystalline phase has been calculated as a function of their lateral distance using a combination of NPT-constant atomistic molecular dynamics calculations (P = 1 atm and T = 310.15 K) and the thermodynamic integration method. The calculated free energy clearly shows that the two cholesterol molecules form a dimer separated by a distance of 1.0-1.5 nm in POPC bilayers. Well depth of the free energy profile is about 3.5 kJ/mol, which is comparable to the thermal energy k(B)T at 310.15 K. This indicates that the aggregation of cholesterol molecules in the bilayers depends on the temperature as well as the concentration of the system. The free energy function obtained here may be used as a reference when coarse grained potential model is investigated for this two-component system. Local structure of POPC molecules around two cholesterol molecules has also been investigated.

An application of improved force field to fully hydrated DPPC and POPC bilayers in a tensionless NPT ensemble: a test of CHARMM 27-based new force field by Högberg et al.

Recently developed all-atom potential model by Högberg et al. has been applied to 1,2-di-palmitoyl-phosphatidylcholine (DPPC) and 1-palmitoryl-2-oleoyl-phosphatidylcholine (POPC) fully hydrated lipid bilayers. Tensionless NPT ensemble calculations have been performed over 40 ns to test the performance of the force field at 1 atm and at 323.15 and 303.15 K, respectively, where we focused our attention on the membrane area and the order parameter. The calculated membrane area per lipid molecule was 0.669 and 0.653 nm2 for DPPC and POPC, respectively, which shows a good agreement with the experimental values 0.642 and 0.683 nm2, respectively. This is an extensive improvement over the original CHARMM 27 or CHARMM 27r, which gives gel-like very small value of the membrane area 0.49 and 0.574 nm2, respectively. Furthermore, the calculated order parameter of C–H vector in acyl tails and electron density profile also show good correspondence with the experiment.

Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Using Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations.

Wide-angle X-ray scattering experiments and all-atomistic molecular dynamics calculations were performed to elucidate the detailed structure of bilayer vesicles constructed by self-assembly of an amphiphilic palladium NCN-pincer complex. We found an excellent agreement between the experimental and calculated X-ray spectra, and between the membrane thickness determined from a TEM image and that calculated from an electron-density profile, which indicated that the calculated structure was highly reliable. The analysis of the simulated bilayer structure showed that in general the membrane was softer than other phospholipid bilayer membranes. In this bilayer assemblage, the degree of alignment of complex molecules in the bilayer membrane was quite low. An analysis of the electron-density profile shows that the bilayer assemblage contains a space through which organic molecules can exit. Furthermore, the catalytically active center is near this space and is easily accessible by organic molecules, which permits the bilayer membrane to act as a nanoreactor. The free energy of permeation of water through the bilayer membrane of the amphiphilic complex was 12 kJ mol-1 , which is much lower than that for phospholipid bilayer membranes in general. Organic molecules are expected to pass though the bilayer membrane. The self-assembled vesicles were shown to be catalytically active in a Miyaura-Michael reaction in water.

Molecular dynamics study of changes in physico-chemical properties of DMPC lipid bilayers by addition of nonionic surfactant C12E10

Changes in physico-chemical properties of dimyristoyl phosphatidylcholine (DMPC) lipid bilayers caused by the addition of 9.4 mol% nonionic surfactant decaoxyethylene monododecyl ethers (C12E10) have been investigated by molecular dynamics calculations. In spite of addition of single chain C12E10, the lipid bilayers showed an increase of membrane area. Isothermal area compressibility, which is a measure of membrane softness in lateral direction, also increased by 50% for DMPC/C12E10 mixed bilayers. Furthermore, the order parameter of C–H vector for DMPC acyl tails decreased. We found that these changes are caused by the hydrophilic head groups of C12E10 which are located near the glycerol backbone of the DMPC molecules and have bulky random coil conformation without any preferential ordered structures.

Structural ordering of lipid bilayers induced by surfactant molecules with small hydrophilic head group

Abstract A series of 100 ns-long molecular dynamics calculations for binary bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 33 mol% ethylene-glycol-ethers () were performed under the isothermal–isobaric condition ( K and atm) to investigate systematically changes in physico-chemical properties of the binary bilayer depending on the length of the hydrophilic head group and the hydrophobic tail. Remarkable differences were observed in membrane properties between the bilayers mixed with surfactants with a large hydrophilic head group and a small hydrophilic head group. In the former, the binary bilayers extended laterally with more disorder in lateral arrangement of the lipid molecules and more disordered acyl tail conformation of the DMPC molecules in the binary bilayers than those in pure DMPC bilayer. In the latter, the bilayers shrunk laterally with more order in lateral arrangement of the lipids and more ordered DMPC acyl tail conformation. The molecular mechanism of these changes in membrane properties is discussed on the basis of two-dimensional radial distribution functions of the lipid mass centres, radius of gyration of lipids and void distribution in membranes. The umbrella effect of phosphocholine head groups was investigated.