Monte Carlo simulations with few DOF’s in large molecules

This Technical Report introduces a data structure and an algorithm to efficiently to efficiently determine rigid clusters in a given molecule. This is a relevant problem in Monte Carlo simulations where the actuated DOFs change at each iteration. If the number of actuated DOFs is small, large temporary rigid groups appear during the time spanned by a MCS step. This document also provides a way of calculating the total energy in the molecules taking into account only inter-rigid energy terms. Thus, a large fraction of energy terms are not required to be computed, namely intra-rigid terms.Postprint (published version

Exploiting single-cycle symmetries in branch-and-prune algorithms

As a first attempt to exploit symmetries in continuous con- straint problems, we focus on permutations of the variables consisting of one single cycle. We propose a procedure that takes advantage of these symmetries by interacting with a Branch-and-Prune algorithm without interfering with it. A key concept in this procedure are the classes of symmetric boxes formed by bisecting a n-dimensional cube at the same point in all dimensions at the same time. We quantify these classes as a function of n. Moreover, we propose a simple algorithm to generate the representatives of all these classes for any number of variables at very high rates. A problem example from the chemical field and a kinematics solver are used to show the performance of the approach in practice.Peer Reviewe

Exploiting single-cycle symmetries in branch-and-prune algorithms

The final publication is available at link.springer.comAs a first attempt to exploit symmetries in continuous constraint problems, we focus on permutations of the variables consisting of one single cycle. We propose a procedure that takes advantage of these symmetries by interacting with a Branch-and-Prune algorithm without interfering with it. A key concept in this procedure are the classes of symmetric boxes formed by bisecting a n-dimensional cube at the same point in all dimensions at the same time. We quantify these classes as a function of n. Moreover, we propose a simple algorithm to generate the representatives of all these classes for any number of variables at very high rates. A problem example from the chemical field and a kinematics solver are used to show the performance of the approach in practice.Peer ReviewedPostprint (author's final draft

Variable symmetry breaking in numerical constraint problems

Symmetry breaking has been a hot topic of research in the past years, leading to many theoretical developments as well as strong scaling strategies for dealing with hard applications. Most of the research has however focused on discrete, combinatorial, problems, and only few considered also continuous, numerical, problems. While part of the theory applies in both contexts, numerical problems have specificities that make most of the technical developments inadequate. In this paper, we present the rlex constraints, partial symmetry-breaking inequalities corresponding to a relaxation of the famous lex constraints extensively studied in the discrete case. They allow (partially) breaking any variable symmetry and can be generated in polynomial time. Contrarily to lex constraints that are impractical in general (due to their overwhelming number) and inappropriate in the continuous context (due to their form), rlex constraints can be efficiently handled natively by numerical constraint solvers. Moreover, we demonstrate their pruning power on continuous domains is almost as strong as that of lex constraints, and they subsume several previous work on breaking specific symmetry classes for continuous problems. Their experimental behavior is assessed on a collection of standard numerical problems and the factors influencing their impact are studied. The results confirm rlex constraints are a dependable counterpart to lex constraints for numerical problems.Peer ReviewedPostprint (author's final draft

Relationship of Weather Types on the Seasonal and Spatial Variability of Rainfall, Runoff, and Sediment Yield in the Western Mediterranean Basin

Rainfall is the key factor to understand soil erosion processes, mechanisms, and rates. Most research was conducted to determine rainfall characteristics and their relationship with soil erosion (erosivity) but there is little information about how atmospheric patterns control soil losses, and this is important to enable sustainable environmental planning and risk prevention. We investigated the temporal and spatial variability of the relationships of rainfall, runoff, and sediment yield with atmospheric patterns (weather types, WTs) in the western Mediterranean basin. For this purpose, we analyzed a large database of rainfall events collected between 1985 and 2015 in 46 experimental plots and catchments with the aim to: (i) evaluate seasonal differences in the contribution of rainfall, runoff, and sediment yield produced by the WTs; and (ii) to analyze the seasonal efficiency of the different WTs (relation frequency and magnitude) related to rainfall, runoff, and sediment yield. The results indicate two different temporal patterns: the first weather type exhibits (during the cold period: autumn and winter) westerly flows that produce the highest rainfall, runoff, and sediment yield values throughout the territory; the second weather type exhibits easterly flows that predominate during the warm period (spring and summer) and it is located on the Mediterranean coast of the Iberian Peninsula. However, the cyclonic situations present high frequency throughout the whole year with a large influence extended around the western Mediterranean basin. Contrary, the anticyclonic situations, despite of its high frequency, do not contribute significantly to the total rainfall, runoff, and sediment (showing the lowest efficiency) because of atmospheric stability that currently characterize this atmospheric pattern. Our approach helps to better understand the relationship of WTs on the seasonal and spatial variability of rainfall, runoff and sediment yield with a regional scale based on the large dataset and number of soil erosion experimental stations

Gestión del conocimiento. Perspectiva multidisciplinaria. Volumen 9

El libro “Gestión del Conocimiento. Perspectiva Multidisciplinaria”, volumen 9, de la Colección Unión Global, es resultado de investigaciones. Los capítulos del libro, son resultados de investigaciones desarrolladas por sus autores. El libro es una publicación internacional, seriada, continua, arbitrada de acceso abierto a todas las áreas del conocimiento, que cuenta con el esfuerzo de investigadores de varios países del mundo, orientada a contribuir con procesos de gestión del conocimiento científico, tecnológico y humanístico que consoliden la transformación del conocimiento en diferentes escenarios, tanto organizacionales como universitarios, para el desarrollo de habilidades cognitivas del quehacer diario. La gestión del conocimiento es un camino para consolidar una plataforma en las empresas públicas o privadas, entidades educativas, organizaciones no gubernamentales, ya sea generando políticas para todas las jerarquías o un modelo de gestión para la administración, donde es fundamental articular el conocimiento, los trabajadores, directivos, el espacio de trabajo, hacia la creación de ambientes propicios para el desarrollo integral de las instituciones

Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.

Background: Data on durability of first-line antiretroviral therapy (ART) in children with human immunodeficiency virus (HIV) are limited. We assessed time to switch to second-line therapy in 16 European countries and Thailand. Methods: Children aged <18 years initiating combination ART (≥2 nucleoside reverse transcriptase inhibitors [NRTIs] plus nonnucleoside reverse transcriptase inhibitor [NNRTI] or boosted protease inhibitor [PI]) were included. Switch to second-line was defined as (i) change across drug class (PI to NNRTI or vice versa) or within PI class plus change of ≥1 NRTI; (ii) change from single to dual PI; or (iii) addition of a new drug class. Cumulative incidence of switch was calculated with death and loss to follow-up as competing risks. Results: Of 3668 children included, median age at ART initiation was 6.1 (interquartile range (IQR), 1.7-10.5) years. Initial regimens were 32% PI based, 34% nevirapine (NVP) based, and 33% efavirenz based. Median duration of follow-up was 5.4 (IQR, 2.9-8.3) years. Cumulative incidence of switch at 5 years was 21% (95% confidence interval, 20%-23%), with significant regional variations. Median time to switch was 30 (IQR, 16-58) months; two-thirds of switches were related to treatment failure. In multivariable analysis, older age, severe immunosuppression and higher viral load (VL) at ART start, and NVP-based initial regimens were associated with increased risk of switch. Conclusions: One in 5 children switched to a second-line regimen by 5 years of ART, with two-thirds failure related. Advanced HIV, older age, and NVP-based regimens were associated with increased risk of switch

Monte Carlo simulations with few DOF’s in large molecules

This Technical Report introduces a data structure and an algorithm to efficiently to efficiently determine rigid clusters in a given molecule. This is a relevant problem in Monte Carlo simulations where the actuated DOFs change at each iteration. If the number of actuated DOFs is small, large temporary rigid groups appear during the time spanned by a MCS step. This document also provides a way of calculating the total energy in the molecules taking into account only inter-rigid energy terms. Thus, a large fraction of energy terms are not required to be computed, namely intra-rigid terms

Monte Carlo simulations with few DOF’s in large molecules

This Technical Report introduces a data structure and an algorithm to efficiently to efficiently determine rigid clusters in a given molecule. This is a relevant problem in Monte Carlo simulations where the actuated DOFs change at each iteration. If the number of actuated DOFs is small, large temporary rigid groups appear during the time spanned by a MCS step. This document also provides a way of calculating the total energy in the molecules taking into account only inter-rigid energy terms. Thus, a large fraction of energy terms are not required to be computed, namely intra-rigid terms

Exploiting single-cycle symmetries in branch-and-prune algorithms

As a first attempt to exploit symmetries in continuous con- straint problems, we focus on permutations of the variables consisting of one single cycle. We propose a procedure that takes advantage of these symmetries by interacting with a Branch-and-Prune algorithm without interfering with it. A key concept in this procedure are the classes of symmetric boxes formed by bisecting a n-dimensional cube at the same point in all dimensions at the same time. We quantify these classes as a function of n. Moreover, we propose a simple algorithm to generate the representatives of all these classes for any number of variables at very high rates. A problem example from the chemical field and a kinematics solver are used to show the performance of the approach in practice.Peer Reviewe