GRAPE-5: A Special-Purpose Computer for N-body Simulation

We have developed a special-purpose computer for gravitational many-body simulations, GRAPE-5. GRAPE-5 is the successor of GRAPE-3. Both consist of eight custom pipeline chips (G5 chip and GRAPE chip). The difference between GRAPE-5 and GRAPE-3 are: (1) The G5 chip contains two pipelines operating at 80 MHz, while the GRAPE chip had one at 20 MHz. Thus, the calculation speed of the G5 chip and that of GRAPE-5 board are 8 times faster than that of GRAPE chip and GRAPE-3 board. (2) The GRAPE-5 board adopted PCI bus as the interface to the host computer instead of VME of GRAPE-3, resulting in the communication speed one order of magnitude faster. (3) In addition to the pure 1/r potential, the G5 chip can calculate forces with arbitrary cutoff functions, so that it can be applied to Ewald or P^3M methods. (4) The pairwise force calculated on GRAPE-5 is about 10 times more accurate than that on GRAPE-3. On one GRAPE-5 board, one timestep of 128k-body simulation with direct summation algorithm takes 14 seconds. With Barnes-Hut tree algorithm (theta = 0.75), one timestep of 10^6-body simulation can be done in 16 seconds.Comment: 19 pages, 24 Postscript figures, 3 tables, Latex, submitted to Publications of the Astronomical Society of Japa

21-residue peptide's dynamics at and between elementary structural transitions

Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions

Molecular phase space transport in water:non-stationary random walk model

Molecular transport in phase space is crucial for chemical reactions because it defines how pre-reactive molecular configurations are found during the time evolution of the system. Using Molecular Dynamics (MD) simulated atomistic trajectories we test the assumption of the normal diffusion in the phase space for bulk water at ambient conditions by checking the equivalence of the transport to the random walk model. Contrary to common expectations we have found that some statistical features of the transport in the phase space differ from those of the normal diffusion models. This implies a non-random character of the path search process by the reacting complexes in water solutions. Our further numerical experiments show that a significant long period of non-stationarity in the transition probabilities of the segments of molecular trajectories can account for the observed non-uniform filling of the phase space. Surprisingly, the characteristic periods in the model non-stationarity constitute hundreds of nanoseconds, that is much longer time scales compared to typical lifetime of known liquid water molecular structures (several picoseconds)

Details of charge distribution in stable viral capsid

We present the results of Molecular Dynamics simulations of a viral capsid with the aim to analyse ion distribution on the capsid's surface that defines its stability. Two systems were modelled, a stable capsid with neutralising number of ions and an unstable capsid with low number of ions. For the ion distribution analysis the capsid's structure was identical and fixed in both simulations. It was then released for the stability analysis. The ion distribution demonstrated two types of the local regions on the inner surface of the capsid's wall: highly occupied with chloride ions in both systems despite a largely uniform electrostatic potential everywhere on the surface, and the regions that loose almost all chloride ions in the unstable capsid. The latter regions are located close to the cracks that are formed when the capsid is destabilised and thus could initiate the collapse of the capsid

Dynamics of Internal Models in Game Players

A new approach for the study of social games and communications is proposed. Games are simulated between cognitive players who build the opponent's internal model and decide their next strategy from predictions based on the model. In this paper, internal models are constructed by the recurrent neural network (RNN), and the iterated prisoner's dilemma game is performed. The RNN allows us to express the internal model in a geometrical shape. The complicated transients of actions are observed before the stable mutually defecting equilibrium is reached. During the transients, the model shape also becomes complicated and often experiences chaotic changes. These new chaotic dynamics of internal models reflect the dynamical and high-dimensional rugged landscape of the internal model space.Comment: 19 pages, 6 figure

Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. Our screening approach employed the molecular mechanics/Poisson-Boltzmann and surface area method to estimate the binding free energies. For the top-ranking 1,000 compounds obtained by docking to a target protein, approximately 6,000 molecular dynamics simulations were performed using multiple docking poses in about a week. As a result, the enrichment performance of the top 100 compounds by our approach was improved by 1.6–4.0 times that of the enrichment performance of molecular dockings. This result indicates that the application of molecular dynamics simulations to virtual screening for lead discovery is both effective and practical. However, further optimization of the computational protocols is required for screening various target proteins