Data compression using correlations and stochastic processes in the ALICE Time Projection chamber

In this paper lossless and a quasi lossless algorithms for the online compression of the data generated by the Time Projection Chamber (TPC) detector of the ALICE experiment at CERN are described. The first algorithm is based on a lossless source code modelling technique, i.e. the original TPC signal information can be reconstructed without errors at the decompression stage. The source model exploits the temporal correlation that is present in the TPC data to reduce the entropy of the source. The second algorithm is based on a lossy source code modelling technique. In order to evaluate the consequences of the error introduced by the lossy compression, the results of the trajectory tracking algorithms that process data offline are analyzed, in particular, with respect to the noise introduced by the compression. The offline analysis has two steps: cluster finder and track finder. The results on how these algorithms are affected by the lossy compression are reported. In both compression technique entropy coding is applied to the set of events defined by the source model to reduce the bit rate to the corresponding source entropy. Using TPC simulated data, the lossless and the lossy compression achieve a data reduction to 49.2% of the original data rate and respectively in the range of 35% down to 30% depending on the desired precision.In this study we have focused on methods which are easy to implement in the frontend TPC electronics.Comment: 8 pages, 3 figures, Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, PSN THLT00

Ions in Fluctuating Channels: Transistors Alive

Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of channels, fluctuating between open conducting, and closed insulating states. Channels control an enormous range of biological function by opening and closing in response to specific stimuli using mechanisms that are not yet understood in physical language. Open channels conduct current of charged particles following laws of Brownian movement of charged spheres rather like the laws of electrodiffusion of quasi-particles in semiconductors. Open channels select between similar ions using a combination of electrostatic and 'crowded charge' (Lennard-Jones) forces. The specific location of atoms and the exact atomic structure of the channel protein seems much less important than certain properties of the structure, namely the volume accessible to ions and the effective density of fixed and polarization charge. There is no sign of other chemical effects like delocalization of electron orbitals between ions and the channel protein. Channels play a role in biology as important as transistors in computers, and they use rather similar physics to perform part of that role. Understanding their fluctuations awaits physical insight into the source of the variance and mathematical analysis of the coupling of the fluctuations to the other components and forces of the system.Comment: Revised version of earlier submission, as invited, refereed, and published by journa

MLAPM - a C code for cosmological simulations

We present a computer code written in C that is designed to simulate structure formation from collisionless matter. The code is purely grid-based and uses a recursively refined Cartesian grid to solve Poisson's equation for the potential, rather than obtaining the potential from a Green's function. Refinements can have arbitrary shapes and in practice closely follow the complex morphology of the density field that evolves. The timestep shortens by a factor two with each successive refinement. It is argued that an appropriate choice of softening length is of great importance and that the softening should be at all points an appropriate multiple of the local inter-particle separation. Unlike tree and P3M codes, multigrid codes automatically satisfy this requirement. We show that at early times and low densities in cosmological simulations, the softening needs to be significantly smaller relative to the inter-particle separation than in virialized regions. Tests of the ability of the code's Poisson solver to recover the gravitational fields of both virialized halos and Zel'dovich waves are presented, as are tests of the code's ability to reproduce analytic solutions for plane-wave evolution. The times required to conduct a LCDM cosmological simulation for various configurations are compared with the times required to complete the same simulation with the ART, AP3M and GADGET codes. The power spectra, halo mass functions and halo-halo correlation functions of simulations conducted with different codes are compared.Comment: 20 pages, 20 figures, MNRAS in press, the code can be downloaded at http://www-thphys.physics.ox.ac.uk/users/MLAPM

Adaptive binning of X-ray galaxy cluster images

We present a simple method for adaptively binning the pixels in an image. The algorithm groups pixels into bins of size such that the fractional error on the photon count in a bin is less than or equal to a threshold value, and the size of the bin is as small as possible. The process is particularly useful for generating surface brightness and colour maps, with clearly defined error maps, from images with a large dynamic range of counts, for example X-ray images of galaxy clusters. We demonstrate the method in application to data from Chandra ACIS-S and ACIS-I observations of the Perseus cluster of galaxies. We use the algorithm to create intensity maps, and colour images which show the relative X-ray intensities in different bands. The colour maps can later be converted, through spectral models, into maps of physical parameters, such as temperature, column density, etc. The adaptive binning algorithm is applicable to a wide range of data, from observations or numerical simulations, and is not limited to two-dimensional data.Comment: 8 pages, 12 figures, accepted by MNRAS (includes changes suggested by referee), high resolution version at http://www-xray.ast.cam.ac.uk/~jss/adbin

The organization of soil disposal by ants

Colonies of Pheidole ambigua ants excavate soil and drop it outside the nest entrance. The deposition of thousands of loads leads to the formation of regular ring-shaped piles. How is this pattern generated? This study investigated soil pile formation on level and sloping surfaces, both empirically and using an agent-based model. We found that ants drop soil preferentially in the direction in which the slope is least steeply uphill from the nest entrance, both when adding to an existing pile and when starting a new pile. Ants respond to cues from local slope to choose downhill directions. Ants walking on a slope increase the frequency and magnitude of changes in direction, and more of these changes of direction take them downhill than uphill. Also, ants carrying soil on a slope wait longer before dropping their soil compared to ants on a level plane. These mechanisms combine to focus soil dropping in the downhill direction, without the necessity of a direct relationship between slope and probability of dropping soil. These empirically determined rules were used to simulate soil disposal. The slight preference for turning downhill measured empirically was shown in the model to be sufficient to generate biologically realistic patterns of soil dumping when combined with memory of the direction of previous trips. From simple rules governing individual behaviour an overall pattern emerges, which is appropriate to the environment and allows a rapid response to changes

Spin Glasses on the Hypercube

We present a mean field model for spin glasses with a natural notion of distance built in, namely, the Edwards-Anderson model on the diluted D-dimensional unit hypercube in the limit of large D. We show that finite D effects are strongly dependent on the connectivity, being much smaller for a fixed coordination number. We solve the non trivial problem of generating these lattices. Afterwards, we numerically study the nonequilibrium dynamics of the mean field spin glass. Our three main findings are: (i) the dynamics is ruled by an infinite number of time-sectors, (ii) the aging dynamics consists on the growth of coherent domains with a non vanishing surface-volume ratio, and (iii) the propagator in Fourier space follows the p^4 law. We study as well finite D effects in the nonequilibrium dynamics, finding that a naive finite size scaling ansatz works surprisingly well.Comment: 14 pages, 22 figure

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd