Thermodynamics of histories for the one-dimensional contact process

The dynamical activity K(t) of a stochastic process is the number of times it changes configuration up to time t. It was recently argued that (spin) glasses are at a first order dynamical transition where histories of low and high activity coexist. We study this transition in the one-dimensional contact process by weighting its histories by exp(sK(t)). We determine the phase diagram and the critical exponents of this model using a recently developed approach to the thermodynamics of histories that is based on the density matrix renormalisation group. We find that for every value of the infection rate, there is a phase transition at a critical value of s. Near the absorbing state phase transition of the contact process, the generating function of the activity shows a scaling behavior similar to that of the free energy in an equilibrium system near criticality.Comment: 16 pages, 7 figure

Bovine tuberculosis surveillance alternatives in Belgium

&lt;p&gt;Belgium obtained the bovine tuberculosis (bTB) officially free status in 2003 (EC Decision 2003/467/EC). This study was carried out to evaluate the components of the current bTB surveillance program in Belgium and to determine the sensitivity of this program. Secondly, alternatives to optimize the bTB surveillance in accordance with European legislation (Council Directive 64/432/EEC) were evaluated. Separate scenario trees were designed for each active surveillance component of the bTB surveillance program. Data from 2005 to 2009 regarding cattle population, movement and surveillance were collected to feed the stochastic scenario tree simulation model. A total of 7,403,826 cattle movement history records were obtained for the 2,678,020 cattle from 36,059 cattle herds still active in 2009. The current surveillance program sensitivity as well as the impact of alternative surveillance protocols was simulated in a stochastic model using 10,000 iterations per simulation. The median (50% percentile) of the component sensitivities across 10,000 iterations was 0.83, 0.85, 0.99, 0.99, respectively, for (i) testing the cattle only during the winter screening, (ii) testing only imported cattle, (iii) testing only purchased cattle and (iv) testing only all slaughtered cattle. The sensitivity analysis showed that the most influential input parameter explaining the variability around the output came from the uncertainty distribution around the sensitivity of the diagnostic tests used within the bTB surveillance. Providing all animals are inspected and post mortem inspection is highly sensitive, slaughterhouse surveillance was the most effective surveillance component. If these conditions were not met, the uncertainty around the mean sensitivity of this component was important. Using an antibody ELISA at purchase and an interferon gamma test during winter screening and at import would increase greatly the sensitivity and the confidence level of Belgium&#039;s freedom from bTB infection status.&lt;/p&gt;</p

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

Absorbing state phase transitions with quenched disorder

Quenched disorder - in the sense of the Harris criterion - is generally a relevant perturbation at an absorbing state phase transition point. Here using a strong disorder renormalization group framework and effective numerical methods we study the properties of random fixed points for systems in the directed percolation universality class. For strong enough disorder the critical behavior is found to be controlled by a strong disorder fixed point, which is isomorph with the fixed point of random quantum Ising systems. In this fixed point dynamical correlations are logarithmically slow and the static critical exponents are conjecturedly exact for one-dimensional systems. The renormalization group scenario is confronted with numerical results on the random contact process in one and two dimensions and satisfactory agreement is found. For weaker disorder the numerical results indicate static critical exponents which vary with the strength of disorder, whereas the dynamical correlations are compatible with two possible scenarios. Either they follow a power-law decay with a varying dynamical exponent, like in random quantum systems, or the dynamical correlations are logarithmically slow even for weak disorder. For models in the parity conserving universality class there is no strong disorder fixed point according to our renormalization group analysis.Comment: 17 pages, 8 figure

Strong disorder fixed point in absorbing state phase transitions

The effect of quenched disorder on non-equilibrium phase transitions in the directed percolation universality class is studied by a strong disorder renormalization group approach and by density matrix renormalization group calculations. We show that for sufficiently strong disorder the critical behaviour is controlled by a strong disorder fixed point and in one dimension the critical exponents are conjectured to be exact: \beta=(3-\sqrt{5})/2 and \nu_\perp=2. For disorder strengths outside the attractive region of this fixed point, disorder dependent critical exponents are detected. Existing numerical results in two dimensions can be interpreted within a similar scenario.Comment: final version as accepted for PRL, contains new results in two dimension

The one-dimensional contact process: duality and renormalisation

We study the one-dimensional contact process in its quantum version using a recently proposed real space renormalisation technique for stochastic many-particle systems. Exploiting the duality and other properties of the model, we can apply the method for cells with up to 37 sites. After suitable extrapolation, we obtain exponent estimates which are comparable in accuracy with the best known in the literature.Comment: 15 page

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Phase transitions in nonequilibrium d-dimensional models with q absorbing states

A nonequilibrium Potts-like model with $q$ absorbing states is studied using Monte Carlo simulations. In two dimensions and $q=3$ the model exhibits a discontinuous transition. For the three-dimensional case and $q=2$ the model exhibits a continuous, transition with $\beta=1$ (mean-field). Simulations are inconclusive, however, in the two-dimensional case for $q=2$. We suggest that in this case the model is close to or at the crossing point of lines separating three different types of phase transitions. The proposed phase diagram in the $(q,d)$ plane is very similar to that of the equilibrium Potts model. In addition, our simulations confirm field-theory prediction that in two dimensions a branching-annihilating random walk model without parity conservation belongs to the directed percolation universality class.Comment: 8 pages, figures included, accepted in Phys.Rev.

Motion of influential players can support cooperation in Prisoner's Dilemma

We study a spatial Prisoner's dilemma game with two types (A and B) of players located on a square lattice. Players following either cooperator or defector strategies play Prisoner's Dilemma games with their 24 nearest neighbors. The players are allowed to adopt one of their neighbor's strategy with a probability dependent on the payoff difference and type of the given neighbor. Players A and B have different efficiency in the transfer of their own strategy therefore the strategy adoption probability is reduced by a multiplicative factor (w < 1) from the players of type B. We report that the motion of the influential payers (type A) can improve remarkably the maintenance of cooperation even for their low densities.Comment: 7 pages, 7 figure

Multicomponent binary spreading process

I investigate numerically the phase transitions of two-component generalizations of binary spreading processes in one dimension. In these models pair annihilation: AA->0, BB->0, explicit particle diffusion and binary pair production processes compete with each other. Several versions with spatially different productions have been explored and shown that for the cases: 2A->3A, 2B->3B and 2A->2AB, 2B->2BA a phase transition occurs at zero production rate ($\sigma=0$), that belongs to the class of N-component, asymmetric branching and annihilating random walks, characterized by the order parameter exponent $\beta=2$. In the model with particle production: AB->ABA, BA-> BAB a phase transition point can be located at $\sigma_c=0.3253$ that belongs to the class of the one-component binary spreading processes.Comment: 5 pages, 5 figure