Fluctuations in Mass-Action Equilibrium of Protein Binding Networks

We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which we refer to as spontaneous, is caused by quickly decaying thermodynamic deviations away from the equilibrium of the system. As such they are amenable to methods of equilibrium statistical mechanics used in our study. We investigate the effects of network connectivity on these fluctuations and compare them to their upper and lower bounds. The collective effects are shown to sometimes lead to large power-law distributed amplification of spontaneous fluctuations as compared to the expectation for isolated dimers. As a consequence of this, the strength of both types of fluctuations is positively correlated with the overall network connectivity of proteins forming the complex. On the other hand, the relative amplitude of fluctuations is negatively correlated with the abundance of the complex. Our general findings are illustrated using a real network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.Comment: 4 pages, 3 figure

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities without losing generality remains a challenge. Here we propose to model cross-feeding interactions at an intermediate level between genome-scale metabolic models of individual species and consumer-resource models of ecosystems, which is suitable to empirical data. We applied our method to three published examples of multi-strain Escherichia coli communities with increasing complexity consisting of uni-, bi-, and multi-directional cross-feeding of either substitutable metabolic byproducts or essential nutrients. The intermediate-scale model accurately described empirical data and could quantify exchange rates elusive by other means, such as the byproduct secretions, even for a complex community of 14 amino acid auxotrophs. We used the three models to study each community's limits of robustness to perturbations such as variations in resource supply, antibiotic treatments and invasion by other "cheaters" species. Our analysis provides a foundation to quantify cross-feeding interactions from experimental data, and highlights the importance of metabolic exchanges in the dynamics and stability of microbial communities.Comment: 6 figure

Expansion Around the Mean-Field Solution of the Bak-Sneppen Model

We study a recently proposed equation for the avalanche distribution in the Bak-Sneppen model. We demonstrate that this equation indirectly relates $\tau$,the exponent for the power law distribution of avalanche sizes, to $D$, the fractal dimension of an avalanche cluster.We compute this relation numerically and approximate it analytically up to the second order of expansion around the mean field exponents. Our results are consistent with Monte Carlo simulations of Bak-Sneppen model in one and two dimensions.Comment: 5 pages, 2 ps-figures iclude

Critical exponents of the anisotropic Bak-Sneppen model

We analyze the behavior of spatially anisotropic Bak-Sneppen model. We demonstrate that a nontrivial relation between critical exponents tau and mu=d/D, recently derived for the isotropic Bak-Sneppen model, holds for its anisotropic version as well. For one-dimensional anisotropic Bak-Sneppen model we derive a novel exact equation for the distribution of avalanche spatial sizes, and extract the value gamma=2 for one of the critical exponents of the model. Other critical exponents are then determined from previously known exponent relations. Our results are in excellent agreement with Monte Carlo simulations of the model as well as with direct numerical integration of the new equation.Comment: 8 pages, three figures included with psfig, some rewriting, + extra figure and table of exponent

Avalanche Dynamics in Evolution, Growth, and Depinning Models

The dynamics of complex systems in nature often occurs in terms of punctuations, or avalanches, rather than following a smooth, gradual path. A comprehensive theory of avalanche dynamics in models of growth, interface depinning, and evolution is presented. Specifically, we include the Bak-Sneppen evolution model, the Sneppen interface depinning model, the Zaitsev flux creep model, invasion percolation, and several other depinning models into a unified treatment encompassing a large class of far from equilibrium processes. The formation of fractal structures, the appearance of $1/f$ noise, diffusion with anomalous Hurst exponents, Levy flights, and punctuated equilibria can all be related to the same underlying avalanche dynamics. This dynamics can be represented as a fractal in $d$ spatial plus one temporal dimension. We develop a scaling theory that relates many of the critical exponents in this broad category of extremal models, representing different universality classes, to two basic exponents characterizing the fractal attractor. The exact equations and the derived set of scaling relations are consistent with numerical simulations of the above mentioned models.Comment: 27 pages in revtex, no figures included. Figures or hard copy of the manuscript supplied on reques

The ALICE experiment at the CERN LHC

ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries. Its overall dimensions are 161626 m3 with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008