Fast Simulation of Facilitated Spin Models

We show how to apply the absorbing Markov chain Monte Carlo algorithm of Novotny to simulate kinetically constrained models of glasses. We consider in detail one-spin facilitated models, such as the East model and its generalizations to arbitrary dimensions. We investigate how to maximise the efficiency of the algorithms, and show that simulation times can be improved on standard continuous time Monte Carlo by several orders of magnitude. We illustrate the method with equilibrium and aging results. These include a study of relaxation times in the East model for dimensions d=1 to d=13, which provides further evidence that the hierarchical relaxation in this model is present in all dimensions. We discuss how the method can be applied to other kinetically constrained models.Comment: 8 pages, 4 figure

Pseudorandom number generation on supercomputers

Random Walks;Supercomputer;computer science

Analytical models of probability distribution and excess noise factor of Solid State Photomultiplier signals with crosstalk

Silicon Photomultipliers (SiPM), also so-called Solid State Photomultipliers (SSPM), are based on Geiger mode avalanche breakdown limited by strong negative feedback. SSPM can detect and resolve single photons due to high gain and ultra-low excess noise of avalanche multiplication in this mode. Crosstalk and afterpulsing processes associated with the high gain introduce specific excess noise and deteriorate photon number resolution of the SSPM. Probabilistic features of these processes are widely studied because of its high importance for the SSPM design, characterization, optimization and application, but the process modeling is mostly based on Monte Carlo simulations and numerical methods. In this study, crosstalk is considered to be a branching Poisson process, and analytical models of probability distribution and excess noise factor (ENF) of SSPM signals based on the Borel distribution as an advance on the geometric distribution models are presented and discussed. The models are found to be in a good agreement with the experimental probability distributions for dark counts and a few photon spectrums in a wide range of fired pixels number as well as with observed super-linear behavior of crosstalk ENF.Comment: 10 pages, 2 tables, 3 figures, Reported at 6th International Conference on "New Developments In Photodetection - NDIP11

Multigrid Monte Carlo Algorithms for SU(2) Lattice Gauge Theory: Two versus Four Dimensions

We study a multigrid method for nonabelian lattice gauge theory, the time slice blocking, in two and four dimensions. For SU(2) gauge fields in two dimensions, critical slowing down is almost completely eliminated by this method. This result is in accordance with theoretical arguments based on the analysis of the scale dependence of acceptance rates for nonlocal Metropolis updates. The generalization of the time slice blocking to SU(2) in four dimensions is investigated analytically and by numerical simulations. Compared to two dimensions, the local disorder in the four dimensional gauge field leads to kinematical problems.Comment: 24 pages, PostScript file (compressed and uuencoded), preprint MS-TPI-94-

On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag