Molecular dynamics simulation on a parallel computer.

For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in Occam 11. The computational nodes of the computer are linked together in a systolic ring. The program based on this .topology for large biopolymers increases its computational throughput nearly linearly with the number of computational nodes. The program developed is closely related to the simulation programs CHARMM and XPLOR, the input files required (force field, protein structure file, coordinates) and output files generated (sets of atomic coordinates representing dynamic trajectories and energies) are compatible with the corresponding files of these programs. Benchmark results of simulations of biopolymers comprising 66, 568, 3 634, 5 797 and 12 637 atoms are compared with XPLOR simulations on conventional computers (Cray, Convex, Vax). These results demonstrate that the software and hardware developed provide extremely cost effective biopolymer simulations. We present also a simulation (equilibrium of X-ray structure) of the complete photosynthetic reaction center of Rhodopseudomonus viridis (12 637 atoms). The simulation accounts for the Coulomb forces exactly, i.e. no cut-off had been assumed

Director's discretionary fund report for FY 1991

The Director's Discretionary Fund (DDF) at the Ames Research Center was established to fund innovative, high-risk projects in basic research which would otherwise be difficult to initiate, but which are essential to our future programs. Here, summaries are given of individual projects within this program. Topics covered include scheduling electric power for the Ames Research Center, the feasibility of light emitting diode arrays as a lighting source for plant growth chambers in space, plasma spraying of nonoxide coatings using a constricted arcjet, and the characterization of vortex impingement footprint using non-intrusive measurement techniques

Domain growth in alloys

This thesis describes Monte-Carlo computer simulations of binary alloys, with comparisons between small angle neutron scattering (SANS) data, and numerically integrated solutions to the Cahn-Hilliard-Cook (CHC) equation. Elementary theories for droplet growth are also compared with computer simulated data. Monte-Carlo dynamical algorithms are investigated in detail, with special regard for universal dynamical times. The computer simulated systems are Fourier transformed to yield partial structure functions which are compared with SANS data for the binary Iron-Chromium system. A relation between real time and simulation time is found. Cluster statistics are measured in the simulated systems, and compared to droplet formation in the Copper-Cobalt system. Some scattering data for the complex steel PE16 is also discussed. The characterisation of domain size and its growth with time are investigated, and scaling laws fitted to real and simulated data. The simple scaling law of Lifshitz and Slyozov is found to be inadequate, and corrections such as those suggested by Huse, are necessary. Scaling behaviour is studied for the low-concentration nucleation regime and the high-concentration spinodal-decomposition regime. The need for multi-scaling is also considered. The effect of noise and fluctuations in the simulations is considered in the MonteCarlo model, a cellular-automaton (CA) model and in the Cahn-Billiard-Cook equation. The Cook noise term in the CHC equation is found to be important for correct growth scaling properties

Molecular dynamics simulations of solid sulphur hexafluoride

This thesis is a study of a molecular crystal SF⁶ through the molecular dynamics(MD) method. Solid SF⁶ has a plastic phase below its melting point and in this phase the interactions between the molecules are highly anharmonic and the orientations of the molecules are highly disordered. At even lower temperatures, the substance has a truly crystalline phase which exhibits, according to our MD simulation, some highly anharmonic properties such as molecular reorientation especially when the temperature is near the plastic -crystal transition point.In the simulation, a simple Lennard -Jones potential function is used to represent the interactions between the molecules. So far, it has been found that this model can give results which are well in agreement with experiments in both the plastic and the crystalline phase. The agreement between the lattice parameters from the simulation and from neutron experiments is very good. The plastic -crystal phase transition and melting are observed in the simulation. The melting point for a bulk sample is found to be 23% higher than the experimental values but the melting point estimated from the surface -initiated melting is found to be closer to the experimental value. In the study of the low- temperature phase we have found that the thermal motions of the molecules are very diferent for the molecules occupying the two different symmetry sites of the monoclinic structure. Highly anisotropic patterns of the molecular movements have also been revealed.In order to study the plastic -crystal phase transition, a constant- pressure MD method is used to ensure the smooth transitions between single -crystals. Through the use of this method, we have found that in the search for new crystalline structures the phase transitions are not necessarily between single crystals - crystallites with certain orientation may prevail resulting in a large crystal with domain structures.SF⁶ is a substance which has not been fully studied through experiments. This offers us an opportunity to use the MD method to predict some of its properties to guide experiments. In this thesis, we present the work on the use the fluctuations of the simulated system to calculate the heat capacity and the elastic constants