Non-equilibrium fluctuations and mechanochemical couplings of a molecular motor

We investigate theoretically the violations of Einstein and Onsager relations, and the efficiency for a single processive motor operating far from equilibrium using an extension of the two-state model introduced by Kafri {\em et al.} [Biophys. J. {\bf 86}, 3373 (2004)]. With the aid of the Fluctuation Theorem, we analyze the general features of these violations and this efficiency and link them to mechanochemical couplings of motors. In particular, an analysis of the experimental data of kinesin using our framework leads to interesting predictions that may serve as a guide for future experiments.Comment: 4 pages, 4 figures, accepted to Phys. Rev. Let

SiGMa: Simple Greedy Matching for Aligning Large Knowledge Bases

The Internet has enabled the creation of a growing number of large-scale knowledge bases in a variety of domains containing complementary information. Tools for automatically aligning these knowledge bases would make it possible to unify many sources of structured knowledge and answer complex queries. However, the efficient alignment of large-scale knowledge bases still poses a considerable challenge. Here, we present Simple Greedy Matching (SiGMa), a simple algorithm for aligning knowledge bases with millions of entities and facts. SiGMa is an iterative propagation algorithm which leverages both the structural information from the relationship graph as well as flexible similarity measures between entity properties in a greedy local search, thus making it scalable. Despite its greedy nature, our experiments indicate that SiGMa can efficiently match some of the world's largest knowledge bases with high precision. We provide additional experiments on benchmark datasets which demonstrate that SiGMa can outperform state-of-the-art approaches both in accuracy and efficiency.Comment: 10 pages + 2 pages appendix; 5 figures -- initial preprin

Coherent Backscattering of light in a magnetic field

This paper describes how coherent backscattering is altered by an external magnetic field. In the theory presented, magneto-optical effects occur inside Mie scatterers embedded in a non-magnetic medium. Unlike previous theories based on point-like scatterers, the decrease of coherent backscattering is obtained in leading order of the magnetic field using rigorous Mie theory. This decrease is strongly enhanced in the proximity of resonances, which cause the path length of the wave inside a scatterer to be increased. Also presented is a novel analysis of the shape of the backscattering cone in a magnetic field.Comment: 27 pages, 5 figures, Revtex, to appear in Phys. Rev.

Modified Fluctuation-dissipation theorem for non-equilibrium steady-states and applications to molecular motors

We present a theoretical framework to understand a modified fluctuation-dissipation theorem valid for systems close to non-equilibrium steady-states and obeying markovian dynamics. We discuss the interpretation of this result in terms of trajectory entropy excess. The framework is illustrated on a simple pedagogical example of a molecular motor. We also derive in this context generalized Green-Kubo relations similar to the ones derived recently by Seifert., Phys. Rev. Lett., 104, 138101 (2010) for more general networks of biomolecular states.Comment: 6 pages, 2 figures, submitted in EP

Local Optimal Sets and Bounded Archiving on Multi-objective NK-Landscapes with Correlated Objectives

The properties of local optimal solutions in multi-objective combinatorial optimization problems are crucial for the effectiveness of local search algorithms, particularly when these algorithms are based on Pareto dominance. Such local search algorithms typically return a set of mutually nondominated Pareto local optimal (PLO) solutions, that is, a PLO-set. This paper investigates two aspects of PLO-sets by means of experiments with Pareto local search (PLS). First, we examine the impact of several problem characteristics on the properties of PLO-sets for multi-objective NK-landscapes with correlated objectives. In particular, we report that either increasing the number of objectives or decreasing the correlation between objectives leads to an exponential increment on the size of PLO-sets, whereas the variable correlation has only a minor effect. Second, we study the running time and the quality reached when using bounding archiving methods to limit the size of the archive handled by PLS, and thus, the maximum size of the PLO-set found. We argue that there is a clear relationship between the running time of PLS and the difficulty of a problem instance.Comment: appears in Parallel Problem Solving from Nature - PPSN XIII, Ljubljana : Slovenia (2014

Local Optimal Sets and Bounded Archiving on Multi-objective NK-Landscapes with Correlated Objectives

The properties of local optimal solutions in multi-objective combinatorial optimization problems are crucial for the effectiveness of local search algorithms, particularly when these algorithms are based on Pareto dominance. Such local search algorithms typically return a set of mutually nondominated Pareto local optimal (PLO) solutions, that is, a PLO-set. This paper investigates two aspects of PLO-sets by means of experiments with Pareto local search (PLS). First, we examine the impact of several problem characteristics on the properties of PLO-sets for multi-objective NK-landscapes with correlated objectives. In particular, we report that either increasing the number of objectives or decreasing the correlation between objectives leads to an exponential increment on the size of PLO-sets, whereas the variable correlation has only a minor effect. Second, we study the running time and the quality reached when using bounding archiving methods to limit the size of the archive handled by PLS, and thus, the maximum size of the PLO-set found. We argue that there is a clear relationship between the running time of PLS and the difficulty of a problem instance.Comment: appears in Parallel Problem Solving from Nature - PPSN XIII, Ljubljana : Slovenia (2014

Assortative mating and differential male mating success in an ash hybrid zone population

BACKGROUND: The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, temporal isolation, variability in phenotypic traits and parasite attacks on the male mating success of two parental species and hybrids by real-time pollen flow analysis. We focus on a hybrid zone population between the two closely related ash species Fraxinus excelsior L. (common ash) and F. angustifolia Vahl (narrow-leaved ash), which is composed of individuals of the two species and several hybrid types. This population is structured by flowering time: the F. excelsior individuals flower later than the F. angustifolia individuals, and the hybrid types flower in-between. Hybrids are scattered throughout the population, suggesting favorable conditions for their local adaptation. We estimate jointly the best-fitting dispersal kernel, the differences in male fecundity due to variation in phenotypic traits and level of parasite attack, and the strength of assortative mating due to differences in flowering phenology. In addition, we assess the effect of accounting for genotyping error on these estimations. RESULTS: We detected a very high pollen immigration rate and a fat-tailed dispersal kernel, counter-balanced by slight phenological assortative mating and short-distance pollen dispersal. Early intermediate flowering hybrids, which had the highest male mating success, showed optimal sex allocation and increased selfing rates. We detected asymmetry of gene flow, with early flowering trees participating more as pollen donors than late flowering trees. CONCLUSION: This study provides striking evidence that long-distance gene flow alone is not sufficient to counter-act the effects of assortative mating and selfing. Phenological assortative mating and short-distance dispersal can create temporal and spatial structuring that appears to maintain this hybrid population. The asymmetry of gene flow, with higher fertility and increased selfing, can potentially confer a selective advantage to early flowering hybrids in the zone. In the event of climate change, hybridization may provide a means for F. angustifolia to further extend its range at the expense of F. excelsior