Relationship between clustering and algorithmic phase transitions in the random k-XORSAT model and its NP-complete extensions

We study the performances of stochastic heuristic search algorithms on Uniquely Extendible Constraint Satisfaction Problems with random inputs. We show that, for any heuristic preserving the Poissonian nature of the underlying instance, the (heuristic-dependent) largest ratio $\alpha_a$ of constraints per variables for which a search algorithm is likely to find solutions is smaller than the critical ratio $\alpha_d$ above which solutions are clustered and highly correlated. In addition we show that the clustering ratio can be reached when the number k of variables per constraints goes to infinity by the so-called Generalized Unit Clause heuristic.Comment: 15 pages, 4 figures, Proceedings of the International Workshop on Statistical-Mechanical Informatics, September 16-19, 2007, Kyoto, Japan; some imprecisions in the previous version have been correcte

Topological Signature of First Order Phase Transitions

We show that the presence and the location of first order phase transitions in a thermodynamic system can be deduced by the study of the topology of the potential energy function, V(q), without introducing any thermodynamic measure. In particular, we present the thermodynamics of an analytically solvable mean-field model with a k-body interaction which -depending on the value of k- displays no transition (k=1), second order (k=2) or first order (k>2) phase transition. This rich behavior is quantitatively retrieved by the investigation of a topological invariant, the Euler characteristic, of some submanifolds of the configuration space. Finally, we conjecture a direct link between the Euler characteristic and the thermodynamic entropy.Comment: 6 pages, 2 figure

La fauna asociada a Tubularia crocea (Agassiz, 1862) (anthomedusae; tubulariidae) y la aplicación de un método de cartificación

A systematic list of the organisms found on the polyps of T. crocea is presented. Monthly samples from the coast of Mar del Plata (38°03'S ; 57°31'W) allowed the analysis of the dynamic of the associations, specially with picnogonids, amphipods, annelids and nematodes, which varied in composition and abundance along of year. We present a modification of a mapping model of Marfenin (1980) and its use to present the different stages of the polyps and the localization of the associated organisms.Se presenta un listado sistemático de los organismos hallados sobre los pólipos de T. creocea. Muestras mensuales obtenidas en la costa de Mar del Plata (38°O8'S ; 57°31'W) permitieron el análisis de la dinámica de las asociaciones, especialmente con picnogónidos, anfípodos, anélidos y nemátodos, las cuales variaron en composición y abundancia a través del año. Nosotros presentamos una modificación del modelo de cartificación de Marfenin (1980) y su uso para representar distintos estados de los pólipos y la localización de los organismos asociados

Can the jamming transition be described using equilibrium statistical mechanics?

When materials such as foams or emulsions are compressed, they display solid behaviour above the so-called `jamming' transition. Because compression is done out-of-equilibrium in the absence of thermal fluctuations, jamming appears as a new kind of a nonequilibrium phase transition. In this proceeding paper, we suggest that tools from equilibrium statistical mechanics can in fact be used to describe many specific features of the jamming transition. Our strategy is to introduce thermal fluctuations and use statistical mechanics to describe the complex phase behaviour of systems of soft repulsive particles, before sending temperature to zero at the end of the calculation. We show that currently available implementations of standard tools such as integral equations, mode-coupling theory, or replica calculations all break down at low temperature and large density, but we suggest that new analytical schemes can be developed to provide a fully microscopic, quantitative description of the jamming transition.Comment: 8 pages, 6 figs. Talk presented at Statphys24 (July 2010, Cairns, Australia

Critical scaling and heterogeneous superdiffusion across the jamming/rigidity transition of a granular glass

The dynamical properties of a dense horizontally vibrated bidisperse granular monolayer are experimentally investigated. The quench protocol produces states with a frozen structure of the assembly, but the remaining degrees of freedom associated with contact dynamics control the appearance of macroscopic rigidity. We provide decisive experimental evidence that this transition is a critical phenomenon, with increasingly collective and heterogeneous rearrangements occurring at length scales much smaller than the grains' diameter, presumably reflecting the contact force network fluctuations. Dynamical correlation time and length scales soar on both sides of the transition, as the volume fraction varies over a remarkably tiny range ($\delta \phi/\phi \sim 10^{-3}$). We characterize the motion of individual grains, which becomes super-diffusive at the jamming transition $\phi_J$, signaling long-ranged temporal correlations. Correspondingly, the system exhibits long-ranged four-point dynamical correlations in space that obey critical scaling at the transition density.Comment: 4 pages, 8 figure

Exact time-average distribution for a stationary non-Markovian massive Brownian particle coupled to two heat baths

Using a time-averaging technique we obtain exactly the probability distribution for position and velocity of a Brownian particle under the influence of two heat baths at different temperatures. These baths are expressed by a white noise term, representing the fast dynamics, and a colored noise term, representing the slow dynamics. Our exact solution scheme accounts for inertial effects, that are not present in approaches that assume the Brownian particle in the over-damped limit. We are also able to obtain the contribution associated with the fast noise that are usually neglected by other approaches.Comment: accepted for publication in Phys. Rev.

Fluctuation theorems for stochastic dynamics

Fluctuation theorems make use of time reversal to make predictions about entropy production in many-body systems far from thermal equilibrium. Here we review the wide variety of distinct, but interconnected, relations that have been derived and investigated theoretically and experimentally. Significantly, we demonstrate, in the context of Markovian stochastic dynamics, how these different fluctuation theorems arise from a simple fundamental time-reversal symmetry of a certain class of observables. Appealing to the notion of Gibbs entropy allows for a microscopic definition of entropy production in terms of these observables. We work with the master equation approach, which leads to a mathematically straightforward proof and provides direct insight into the probabilistic meaning of the quantities involved. Finally, we point to some experiments that elucidate the practical significance of fluctuation relations.Comment: 48 pages, 2 figures. v2: minor changes for consistency with published versio

Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism

Two-state models provide phenomenological descriptions of many different systems, ranging from physics to chemistry and biology. We investigate work fluctuations in an ensemble of two-state systems driven out of equilibrium under the action of an external perturbation. We calculate the probability density P(W) that a work equal to W is exerted upon the system along a given non-equilibrium trajectory and introduce a trajectory thermodynamics formalism to quantify work fluctuations in the large-size limit. We then define a trajectory entropy S(W) that counts the number of non-equilibrium trajectories P(W)=exp(S(W)/kT) with work equal to W. A trajectory free-energy F(W) can also be defined, which has a minimum at a value of the work that has to be efficiently sampled to quantitatively test the Jarzynski equality. Within this formalism a Lagrange multiplier is also introduced, the inverse of which plays the role of a trajectory temperature. Our solution for P(W) exactly satisfies the fluctuation theorem by Crooks and allows us to investigate heat-fluctuations for a protocol that is invariant under time reversal. The heat distribution is then characterized by a Gaussian component (describing small and frequent heat exchange events) and exponential tails (describing the statistics of large deviations and rare events). For the latter, the width of the exponential tails is related to the aforementioned trajectory temperature. Finite-size effects to the large-N theory and the recovery of work distributions for finite N are also discussed. Finally, we pay particular attention to the case of magnetic nanoparticle systems under the action of a magnetic field H where work and heat fluctuations are predicted to be observable in ramping experiments in micro-SQUIDs.Comment: 28 pages, 14 figures (Latex

On the range of validity of the fluctuation theorem for stochastic Markovian dynamics

We consider the fluctuations of generalized currents in stochastic Markovian dynamics. The large deviations of current fluctuations are shown to obey a Gallavotti-Cohen (GC) type symmetry in systems with a finite state space. However, this symmetry is not guaranteed to hold in systems with an infinite state space. A simple example of such a case is the Zero-Range Process (ZRP). Here we discuss in more detail the already reported breakdown of the GC symmetry in the context of the ZRP with open boundaries and we give a physical interpretation of the phases that appear. Furthermore, the earlier analytical results for the single-site case are extended to cover multiple-site systems. We also use our exact results to test an efficient numerical algorithm of Giardina, Kurchan and Peliti, which was developed to measure the current large deviation function directly. We find that this method breaks down in some phases which we associate with the gapless spectrum of an effective Hamiltonian.Comment: 37 pages, 10 figures. Minor alterations, fixed typos (as appeared in JSTAT

Identification of Giardia lamblia DHHC Proteins and the Role of Protein S-palmitoylation in the Encystation Process

Protein S-palmitoylation, a hydrophobic post-translational modification, is performed by protein acyltransferases that have a common DHHC Cys-rich domain (DHHC proteins), and provides a regulatory switch for protein membrane association. In this work, we analyzed the presence of DHHC proteins in the protozoa parasite Giardia lamblia and the function of the reversible S-palmitoylation of proteins during parasite differentiation into cyst. Two specific events were observed: encysting cells displayed a larger amount of palmitoylated proteins, and parasites treated with palmitoylation inhibitors produced a reduced number of mature cysts. With bioinformatics tools, we found nine DHHC proteins, potential protein acyltransferases, in the Giardia proteome. These proteins displayed a conserved structure when compared to different organisms and are distributed in different monophyletic clades. Although all Giardia DHHC proteins were found to be present in trophozoites and encysting cells, these proteins showed a different intracellular localization in trophozoites and seemed to be differently involved in the encystation process when they were overexpressed. dhhc transgenic parasites showed a different pattern of cyst wall protein expression and yielded different amounts of mature cysts when they were induced to encyst. Our findings disclosed some important issues regarding the role of DHHC proteins and palmitoylation during Giardia encystation.Fil: Merino, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Zamponi, Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Vranych, Cecilia Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Touz, Maria Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Ropolo, Andrea Silvana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin