Self-organisation to criticality in a system without conservation law

We numerically investigate the approach to the stationary state in the nonconservative Olami-Feder-Christensen (OFC) model for earthquakes. Starting from initially random configurations, we monitor the average earthquake size in different portions of the system as a function of time (the time is defined as the input energy per site in the system). We find that the process of self-organisation develops from the boundaries of the system and it is controlled by a dynamical critical exponent z~1.3 that appears to be universal over a range of dissipation levels of the local dynamics. We show moreover that the transient time of the system $t_{tr}$ scales with system size L as $t_{tr} \sim L^z$. We argue that the (non-trivial) scaling of the transient time in the OFC model is associated to the establishment of long-range spatial correlations in the steady state.Comment: 10 pages, 6 figures; accepted for publication in Journal of Physics

Docking protein domains in contact space

BACKGROUND: Many biological processes involve the physical interaction between protein domains. Understanding these functional associations requires knowledge of the molecular structure. Experimental investigations though present considerable difficulties and there is therefore a need for accurate and reliable computational methods. In this paper we present a novel method that seeks to dock protein domains using a contact map representation. Rather than providing a full three dimensional model of the complex, the method predicts contacting residues across the interface. We use a scoring function that combines structural, physicochemical and evolutionary information, where each potential residue contact is assigned a value according to the scoring function and the hypothesis is that the real configuration of contacts is the one that maximizes the score. The search is performed with a simulated annealing algorithm directly in contact space. RESULTS: We have tested the method on interacting domain pairs that are part of the same protein (intra-molecular domains). We show that it correctly predicts some contacts and that predicted residues tend to be significantly closer to each other than other pairs of residues in the same domains. Moreover we find that predicted contacts can often discriminate the best model (or the native structure, if present) among a set of optimal solutions generated by a standard docking procedure. CONCLUSION: Contact docking appears feasible and able to complement other computational methods for the prediction of protein-protein interactions. With respect to more standard docking algorithms it might be more suitable to handle protein conformational changes and to predict complexes starting from protein models

Degree of Hydrolysis Affects the Techno-Functional Properties of Lesser Mealworm Protein Hydrolysates

Protein hydrolysates from lesser mealworm (Alphitobius diaperinus, LM) were obtained by enzymatic hydrolysis with protease from Bacillus licheniformis. A preliminary test performed for five hours of hydrolysis generated an insect protein hydrolysate with 15% of degree of hydrolysis (DH), optimum solubility property and oil holding capacity, but emulsifying and foaming ability were completely impaired. In order to investigate the potential implication of DH on techno-functional properties, a set of protein hydrolysates with a different DH was obtained by sub-sampling at different time points during three hours of enzymatic hydrolysis process. An increase in DH% had positive effects on the solubility property and oil holding ability, while a reduced emulsifying ability was observed up to five hours of hydrolysis. These results demonstrated that the enzymatic hydrolysis, if performed under controlled conditions and not for a long period, represents a valid method to extract high quality protein from insects with tailored techno-functionality, in order to produce tailored ingredients for feed and food purpose

The geography of metapopulation synchrony in dendritic river networks

Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time-series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality generate fundamental spatial patterns of synchrony in fish metapopulations, empirical synchrograms can aid knowledge advancement and inform conservation strategies in complex habitatsinfo:eu-repo/semantics/publishedVersio

Emergence of an MDR Klebsiella pneumoniae ST231 producing OXA-232 and RmtF in Switzerland

The increasing incidence of carbapenem-resistant Klebsiella pneumoniae is a major challenge to public health. Despite the fact that the prevalence of carbapenemases among carbapenem-resistant K. pneumoniae varies geographically, the incidence of OXA-48-like enzymes has soared in recent years and is particularly high in some European countries, such as Spain and France (74% and 78% among carbapenemase-producing K. pneumoniae, respectively).1 A significant number of OXA-48 variants have been reported in the last decade. This includes OXA-232, a carbapenemase firstly identified in France in 20112 and thereafter found in several countries.3,4 Recently, an MDR K. pneumoniae ST231 co-producing OXA-232, the ESBL CTX-M-15 and the 16S rRNA methyltransferase RmtF conferring broad- spectrum resistance to aminoglycosides has emerged as a successful epidemic..

Boundary effects in a random neighbor model of earthquakes

We introduce spatial inhomogeneities (boundaries) in a random neighbor version of the Olami, Feder and Christensen model [Phys. Rev. Lett. 68, 1244 (1992)] and study the distributions of avalanches starting both from the bulk and from the boundaries of the system. Because of their clear geophysical interpretation, two different boundary conditions have been considered (named free and open, respectively). In both cases the bulk distribution is described by the exponent $\tau \simeq {3/2}$. Boundary distributions are instead characterized by two different exponents $\tau ' \simeq {3/2}$ and $\tau ' \simeq {7/4}$, for free and open boundary conditions, respectively. These exponents indicate that the mean-field behavior of this model is correctly described by a recently proposed inhomogeneous form of critical branching process.Comment: 6 pages, 2 figures ; to appear on PR

Scaling in a Nonconservative Earthquake Model of Self-Organised Criticality

We numerically investigate the Olami-Feder-Christensen model for earthquakes in order to characterise its scaling behaviour. We show that ordinary finite size scaling in the model is violated due to global, system wide events. Nevertheless we find that subsystems of linear dimension small compared to the overall system size obey finite (subsystem) size scaling, with universal critical coefficients, for the earthquake events localised within the subsystem. We provide evidence, moreover, that large earthquakes responsible for breaking finite size scaling are initiated predominantly near the boundary.Comment: 6 pages, 6 figures, to be published in Phys. Rev. E; references sorted correctl