Convexity deficit of benzenoids

In 2012, a family of benzenoids was introduced by Cruz, Gutman, and Rada, which they called convex benzenoids. In this paper we introduce the convexity deficit, a new topological index intended for benzenoids and, more generally, fusenes. This index measures by how much a given fusene departs from convexity. It is defined in terms of the boundary-edges code. In particular, convex benzenoids are exactly the benzenoids having convexity deficit equal to 0. Quasi-convex benzenoids form the family of non-convex benzenoids that are closest to convex, i.e., they have convexity deficit equal to 1. Finally, we investigate convexity deficit of several important families of benzenoids

Elementary landscape decomposition of the 0-1 unconstrained quadratic optimization

Journal of Heuristics, 19(4), pp.711-728Landscapes’ theory provides a formal framework in which combinatorial optimization problems can be theoretically characterized as a sum of an especial kind of landscape called elementary landscape. The elementary landscape decomposition of a combinatorial optimization problem is a useful tool for understanding the problem. Such decomposition provides an additional knowledge on the problem that can be exploited to explain the behavior of some existing algorithms when they are applied to the problem or to create new search methods for the problem. In this paper we analyze the 0-1 Unconstrained Quadratic Optimization from the point of view of landscapes’ theory. We prove that the problem can be written as the sum of two elementary components and we give the exact expressions for these components. We use the landscape decomposition to compute autocorrelation measures of the problem, and show some practical applications of the decomposition.Spanish Ministry of Sci- ence and Innovation and FEDER under contract TIN2008-06491-C04-01 (the M∗ project). Andalusian Government under contract P07-TIC-03044 (DIRICOM project)

A simple two-module problem to exemplify building-block assembly under crossover

Theoretically and empirically it is clear that a genetic algorithm with crossover will outperform a genetic algorithm without crossover in some fitness landscapes, and vice versa in other landscapes. Despite an extensive literature on the subject, and recent proofs of a principled distinction in the abilities of crossover and non-crossover algorithms for a particular theoretical landscape, building general intuitions about when and why crossover performs well when it does is a different matter. In particular, the proposal that crossover might enable the assembly of good building-blocks has been difficult to verify despite many attempts at idealized building-block landscapes. Here we show the first example of a two-module problem that shows a principled advantage for cross-over. This allows us to understand building-block assembly under crossover quite straightforwardly and build intuition about more general landscape classes favoring crossover or disfavoring it

High intensity tapping regime in a frustrated lattice gas model of granular compaction

In the frame of a well established lattice gas model for granular compaction, we investigate the high intensity tapping regime where a pile expands significantly during external excitation. We find that this model shows the same general trends as more sophisticated models based on molecular dynamic type simulations. In particular, a minimum in packing fraction as a function of tapping strength is observed in the reversible branch of an annealed tapping protocol.Comment: 5 pages, 4 figure

Analysis of three-nucleon forces effects in the A=3A=3 system

Using modern nucleon-nucleon interactions in the description of the $A=3,4$ nuclear systems the $\chi^2$ per datum results to be much bigger than one. In particular it is not possible to reproduce the three- and four-nucleon binding energies and the $n-d$ scattering length simultaneously. This is one manifestation of the necessity of including a three-nucleon force in the nuclear Hamiltonian. In this paper we perform an analysis of some, widely used, three-nucleon force models. We analyze their capability to describe the aforementioned quantities and, to improve their description, we propose modifications in the parametrization of the models. The effects of these new parametrization are studied in some polarization observables at low energies.Comment: 10 pages, to be published in Few-Body Systems. Presented at the workshop on "Relativistic Description of Two- and Three-body Systems in Nuclear Physics" ECT* Trento, 19 - 23 October 200

The effects of grain shape and frustration in a granular column near jamming

We investigate the full phase diagram of a column of grains near jamming, as a function of varying levels of frustration. Frustration is modelled by the effect of two opposing fields on a grain, due respectively to grains above and below it. The resulting four dynamical regimes (ballistic, logarithmic, activated and glassy) are characterised by means of the jamming time of zero-temperature dynamics, and of the statistics of attractors reached by the latter. Shape effects are most pronounced in the cases of strong and weak frustration, and essentially disappear around a mean-field point.Comment: 17 pages, 19 figure

The alpha-particle based on modern nuclear forces

The Faddeev-Yakubovsky equations for the alpha-particle are solved. Accurate results are obtained for several modern NN interaction models, which include charge-symmetry breaking effects in the NN force, nucleon mass dependences as well as the Coulomb interaction. These models are augmented by three-nucleon forces of different types and adjusted to the 3N binding energy. Our results are close to the experimental binding energy with a slight overbinding. Thus there is only little room left for the contribution of possible 4N interactions to the alpha-particle binding energy. We also discuss model dependences of the binding energies and the wave functions.Comment: 22 pages REVTeX 4, 12 figures, table with TM parameters added, typos corrected, version as published in PR

Glassy dynamics in granular compaction: sand on random graphs

We discuss the use of a ferromagnetic spin model on a random graph to model granular compaction. A multi-spin interaction is used to capture the competition between local and global satisfaction of constraints characteristic for geometric frustration. We define an athermal dynamics designed to model repeated taps of a given strength. Amplitude cycling and the effect of permanently constraining a subset of the spins at a given amplitude is discussed. Finally we check the validity of Edwards' hypothesis for the athermal tapping dynamics.Comment: 13 pages Revtex, minor changes, to appear in PR

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench

The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis