Radiation Magnetohydrodynamics Simulation of Proto-Stellar Collapse: Two-Component Molecular Outflow

We perform a three-dimensional nested-grid radiation magneto-hydrodynamics (RMHD) simulation with self-gravity to study the early phase of the low-mass star formation process from a rotating molecular cloud core to a first adiabatic core just before the second collapse begins. Radiation transfer is handled with the flux-limited diffusion approximation, operator-splitting and implicit time-integrator. In the RMHD simulation, the outer region of the first core attains a higher entropy and the size of first core is larger than that in the magnetohydrodynamics simulations with the barotropic approximation. Bipolar molecular outflow consisting of two components is driven by magnetic Lorentz force via different mechanisms, and shock heating by the outflow is observed. Using the RMHD simulation we can predict and interpret the observed properties of star-forming clouds, first cores and outflows with millimeter/submillimeter radio interferometers, especially the Atacama Large Millimeter/submillimeter Array (ALMA).Comment: 13 pages, 5 figures, submitted to ApJ

Grid computing and molecular simulations: the vision of the eMinerals Project

This paper discusses a number of aspects of using grid computing methods in support of molecular simulations, with examples drawn from the eMinerals project. A number of components for a useful grid infrastructure are discussed, including the integration of compute and data grids, automatic metadata capture from simulation studies, interoperability of data between simulation codes, management of data and data accessibility, management of jobs and workflow, and tools to support collaboration. Use of a grid infrastructure also brings certain challenges, which are discussed. These include making use of boundless computing resources, the necessary changes, and the need to be able to manage experimentation

Fourier Acceleration of Langevin Molecular Dynamics

Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is based on a mapping of the particles' dynamics to a regular grid so that discrete Fourier transforms may be taken, it should be emphasized that the introduction of the grid is a purely algorithmic device and that no smoothing, coarse-graining or mean-field approximations are made. The method thus can be applied to the equations of motion of molecular dynamics (MD), or its Langevin or Brownian variants. For example, in Langevin MD simulations our acceleration technique permits a straightforward spectral decomposition of forces so that the long-wavelength modes are integrated with a longer time step, thereby reducing the time required to reach equilibrium or to decorrelate the system in equilibrium. Speedup factors of up to 30 are observed relative to pure (unaccelerated) Langevin MD. As with acceleration of critical lattice models, even further gains relative to the unaccelerated method are expected for larger systems. Preliminary results for Fourier-accelerated molecular dynamics are presented in order to illustrate the basic concepts. Possible extensions of the method and further lines of research are discussed.Comment: 11 pages, two illustrations included using graphic

DOF phase separation of the Lennard-Jones fcc(111) surface

Recent lattice model calculations have suggested that a full-layered crystal surface may undergo, under canonical (particle-conserving) conditions, a preroughening-driven two-dimensional phase separation into two disordered flat (DOF) regions, of opposite order parameter. We have carried out extensive classical molecular dynamics (MD) simulations of the Lennard-Jones fcc(111) surface, to check whether these predictions are relevant or not for a realistic continuous system. Very long simulation times, a grid of temperatures from (2/3)Tm to Tm, and unusually large system sizes are employed to ensure full equilibrium and good statistics. By examining layer-by-layer occupancies, height fluctuations, sublattice order parameter and X-ray structure factors, we find a clear anomaly at ~0.83Tm. The anomaly is distinct from roughening (whose incipiency is also detected at ~0.94Tm), and is seen to be consistent with the preroughening plus phase separation scenario.Comment: REVTeX, 8 pages, 4 figures; new figure showing simulation snapshots added; reference updated and other minor change

A Thermodynamically-Consistent Non-Ideal Stochastic Hard-Sphere Fluid

A grid-free variant of the Direct Simulation Monte Carlo (DSMC) method is proposed, named the Isotropic DSMC (I-DSMC) method, that is suitable for simulating dense fluid flows at molecular scales. The I-DSMC algorithm eliminates all grid artifacts from the traditional DSMC algorithm; it is Galilean invariant and microscopically isotropic. The stochastic collision rules in I-DSMC are modified to yield a non-ideal structure factor that gives consistent compressibility, as first proposed in [Phys. Rev. Lett. 101:075902 (2008)]. The resulting Stochastic Hard Sphere Dynamics (SHSD) fluid is empirically shown to be thermodynamically identical to a deterministic Hamiltonian system of penetrable spheres interacting with a linear core pair potential, well-described by the hypernetted chain (HNC) approximation. We apply a stochastic Enskog kinetic theory for the SHSD fluid to obtain estimates for the transport coefficients that are in excellent agreement with particle simulations over a wide range of densities and collision rates. The fluctuating hydrodynamic behavior of the SHSD fluid is verified by comparing its dynamic structure factor against theory based on the Landau-Lifshitz Navier-Stokes equations. We also study the Brownian motion of a nano-particle suspended in an SHSD fluid and find a long-time power-law tail in its velocity autocorrelation function consistent with hydrodynamic theory and molecular dynamics calculations.Comment: 30 pages, revision adding some clarifications and a new figure. See also arXiv:0803.035