Performance of the Cell processor for biomolecular simulations

The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for the non-bonded force calculations, over one order of magnitude faster than a single core standard processor

Systematic coarse graining: "Four lessons and a caveat" from nonequilibrium statistical mechanics

With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained information for dynamic systems. We sketch the role and potential of Monte Carlo, molecular dynamics and Brownian dynamics simulations in the thermodynamic approach to coarse graining. A melt of entangled linear polyethylene molecules serves us as an illustrative example.Comment: 15 pages, 4 figure

Geodetic Observations of Weak Determinism in Rupture Evolution of Large Earthquakes.

The moment evolution of large earthquakes is a subject of fundamental interest to both basic and applied seismology. Specifically, an open problem is when in the rupture process a large earthquake exhibits features dissimilar from those of a lesser magnitude event. The answer to this question is of importance for rapid, reliable estimation of earthquake magnitude, a major priority of earthquake and tsunami early warning systems. Much effort has been made to test whether earthquakes are deterministic, meaning that observations in the first few seconds of rupture can be used to predict the final rupture extent. However, results have been inconclusive, especially for large earthquakes greater than M w 7. Traditional seismic methods struggle to rapidly distinguish the size of large-magnitude events, in particular near the source, even after rupture completion, making them insufficient to resolve the question of predictive rupture behavior. Displacements derived from Global Navigation Satellite System data can accurately estimate magnitude in real time, even for the largest earthquakes. We employ a combination of seismic and geodetic (Global Navigation Satellite System) data to investigate early rupture metrics, to determine whether observational data support deterministic rupture behavior. We find that while the earliest metrics (~5 s of data) are not enough to infer final earthquake magnitude, accurate estimates are possible within the first tens of seconds, prior to rupture completion, suggesting a weak determinism. We discuss the implications for earthquake source physics and rupture evolution and address recommendations for earthquake and tsunami early warning

Simulating Hard Rigid Bodies

Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in condensed matter. The next level of description is to consider particles as rigid objects of generic shape, which would enrich the possible phenomenology enormously. This kind of modeling will prove to be interesting in all those situations in which steric effects play a relevant role. These include biology, soft matter, granular materials and molecular systems. With a view to developing a general recipe for event-driven Molecular Dynamics simulations of hard rigid bodies, two algorithms for calculating the distance between two convex hard rigid bodies and the contact time of two colliding hard rigid bodies solving a non-linear set of equations will be described. Building on these two methods, an event-driven molecular dynamics algorithm for simulating systems of convex hard rigid bodies will be developed and illustrated in details. In order to optimize the collision detection between very elongated hard rigid bodies, a novel nearest-neighbor list method based on an oriented bounding box will be introduced and fully explained. Efficiency and performance of the new algorithm proposed will be extensively tested for uniaxial hard ellipsoids and superquadrics. Finally applications in various scientific fields will be reported and discussed.Comment: 36 pages, 17 figure

The volume densities of giant molecular clouds in M83

Using observed GALEX far-ultraviolet (FUV) fluxes and VLA images of the 21-cm HI column densities, along with estimates of the local dust abundances, we measure the volume densities of a sample of actively star-forming giant molecular clouds (GMCs) in the nearby spiral galaxy M83 on a typical resolution scale of 170 pc. Our approach is based on an equilibrium model for the cycle of molecular hydrogen formation on dust grains and photodissociation under the influence of the FUV radiation on the cloud surfaces of GMCs. We find a range of total volume densities on the surface of GMCs in M83, namely 0.1 - 400 cm-3 inside R25, 0.5 - 50 cm-3 outside R25 . Our data include a number of GMCs in the HI ring surrounding this galaxy. Finally, we discuss the effects of observational selection, which may bias our results.Comment: 9 pages, 11 figure

XMM-Newton observation of the relaxed cluster A478: gas and dark matter distribution from 0.01 R_200 to 0.5 R_200

We present an \xmm mosaic observation of the hot ($kT\sim6.5$ keV) and nearby ($z=0.0881$) relaxed cluster of galaxies A478. We derive precise gas density, gas temperature, gas mass and total mass profiles up to 12\arcmin (about half of the virial radius $R_{200}$). The gas density profile is highly peaked towards the center and the surface brightness profile is well fitted by a sum of three $\beta$--models. The derived gas density profile is in excellent agreement, both in shape and in normalization, with the published Chandra density profile (measured within 5\arcmin of the center). Projection and PSF effects on the temperature profile determination are thoroughly investigated. The derived radial temperature structure is as expected for a cluster hosting a cooling core, with a strong negative gradient at the cluster center. The temperature rises from $\sim2$ keV up to a plateau of $\sim6.5$ keV beyond 2' (i.e. $r>208\rm{kpc}=0.1 R_{200}$, $R_{200}=2.08$ Mpc being the virial radius). From the temperature profile and the density profile and under the hypothesis of hydrostatic equilibrium, we derived the total mass profile of A478 down to 0.01 and up to 0.5 the virial radius. We tested different dark matter models against the observed mass profile. The Navarro, Frenk & White (\cite{navarro97}) model is significantly preferred to other models. It leads to a total mass of $M_{200}=1.1\times 10^{15}$ M$_\odot$ for a concentration parameter of $c=4.2\pm0.4$. The gas mass fraction slightly increases with radius. The gas mass fraction at a density contrast of $\delta=2500$ is \fgas=0.13\pm0.02, consistent with previous results on similar hot and massive clusters. We confirm the excess of absorption in the direction of A478.[abridged]Comment: 15 pages, 11 figures, accepted for publication in A&A, corrected typo

Dynamics of uniaxial hard ellipsoids

We study the dynamics of monodisperse hard ellipsoids via a new event-driven molecular dynamics algorithm as a function of volume fraction $\phi$ and aspect ratio $X_0$. We evaluate the translational $D_{trans}$ and the rotational $D_{rot}$ diffusion coefficient and the associated isodiffusivity lines in the $\phi-X_0$ plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the $D_{trans}$ and $D_{rot}$ isodiffusivity lines. While the self intermediate scattering function exhibits stretched relaxation, i.e. glassy dynamics, only for large $\phi$ and $X_0 \approx 1$, the second order orientational correlator $C_2(t)$ shows stretching only for large and small $X_0$ values. We discuss these findings in the context of a possible pre-nematic order driven glass transition.Comment: accepted by Phys. Rev. Let