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.

SUMMARYA simplified method of numerical analysis has been developed to estimate the deformation and load distribution of piled raft foundations subjected to ground movements induced by tunnelling and incorporated into a computer program 'PRAB'. In this method, a hybrid model is employed in which the flexible raft is modelled as thin plates, the piles as elastic beams, and the soil is treated as interactive springs. The interactions between structural members, pile-soil-pile, pile-soil-raft and raft-soil-raft interactions, are modelled based on Mindlin's solutions for both vertical and lateral forces. The validity of the proposed method is verified through comparisons with some published solutions for single piles and pile groups subjected to ground movements induced by tunnelling. Thereafter, the solutions from this approach for the analysis of a pile group and a piled raft subjected to ground movements induced by tunnelling are compared with those from three-dimensional finite difference program. Good agreements between these solutions are demonstrated. The method is then used for a parametric study of single piles, pile groups and piled rafts subjected to ground movements induced by tunnelling.

Data are presented for photospallation yields from "^Au, '"La, '"Cs, '"I, ®'Y, "Co and "V targets measured at bremsstrahlung end-point energies (£0) from 30 to 1050 MeV in steps of 100 MeV or less with the aid of suitable radiochemical Separation. The measurements were performed for 40 nuclides from "^Au, 52 from '"La, 44 from '"Cs, 28 from '"I, 31 from ®'Y, 27 from "Co and 22 from "V. The observed yields were either independent or cumulative. For the latter, the precursor-corrected values are also presented. The present results are compared with the available literature data in a form of EQdependence. Isomer yield ratios for 38 pairs were also studied in terms of EQ-, target mass-and spin-dependence.

We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. [2000] Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.

Ultra-long-chain fatty acids (ULCFAs) are biosynthesized in the restricted tissues such as retina, testis, and skin. The conformation of a single ULCFA, in which the sn-1 unsaturated chain has 32 carbons, in three types of phospholipid bilayers is studied by molecular dynamics simulations. It is found that the ultra-long tail of the ULCFA flips between two leaflets and fluctuates among an elongation into the opposite leaflet, lies between two leaflets, and turns back. As the number ratio of lipids in the opposite leaflet increases, the ratio of the elongated shape linearly decreases in all three cases. Thus, ULCFAs can sense the density differences between the two leaflets and respond to these changes.

Monte Carlo calculations based on the PICA (Photon-Induced Intranuclear Cascade Analysis) code by Gabriel and Alsmiller have been performed for bremsstrahlung-induced spallation of 51 V, 59 Co, 89 Y, 127 1, 133 Cs, 139 La and 197 Au at bremsstrahlung end-point energies of 200 -400 MeV and compared with the experimental results reported in part I of this series of work and others and with the empirical ones reported in part II. The gross features of the experimental and empirical mass and isotopic distributions were found to be reproduced by the PICA code qualitatively for lighter targets of mass = 51-89, but not for heavier targets. The limitations of the reproducibility by the PICA code were examined. The total photoabsorption cross sections are also discussed.

Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important, as is the atomic description of the series of conformational changes associated with the photocycle. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42, suggesting that this atom is the focus of the protein quake of PYP. This is consistent with previous experimental observations.

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