MoMA-LigPath: A web server to simulate protein-ligand unbinding

Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity. However, obtaining information about these interactions with experimental or computational methods remains difficult. The computational tool presented in this paper, MoMA-LigPath, is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space. Such a purely geometric approach, together with the efficiency of the exploration algorithm, enables the simulation of ligand unbinding within very short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide very useful information about protein-ligand interactions. When needed, this approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. MoMA-LigPath is available at http://moma.laas.fr. The web server is free and open to all users, with no login requirement

Frequency and voltage partitioning in presence of renewable energy resources for power system (example: North Chile power network)

This paper investigates techniques for frequency and voltage partitioning of power network based on the graph-theory. These methods divide the power system into distinguished regions to avoid the spread of disturbances and to minimize the interaction between these regions for frequency and voltage control of power system. In case of required active and reactive power for improving the performance of the power system, control can be performed regionally instead of a centralized controller. In this paper, renewable energy sources are connected to the power network to verify the effect of these sources on the power systems partitioning and performance. The number of regions is found based on the frequency sensitivity for frequency partitioning and bus voltage for voltage partitioning to disturbances being applied to loads in each region. The methodology is applied to the north part of Chile power network. The results show the performance and ability of graph frequency and voltage partitioning algorithm to divide large scale power systems to smaller regions for applying decentralized controllers.Peer ReviewedPostprint (published version

Global Saturated Regulator with Variable Gains for Robot Manipulators

In this paper, we propose a set of saturated controllers with variable gains to solve the regulation problem for robot manipulators in joint space. These control schemes deliver torques inside the prescribed limits of servomotors. The gamma of variable gains is formed by continuous, smooth, and differentiable functions of the joint position error and velocity of the manipulator. A strict Lyapunov function is proposed to demonstrate globally asymptotic stability of the closed-loop equilibrium point. Finally, the functionality and performance of the proposal are illustrated via simulation results and comparative analysis against Proportional-Derivative (PD) control scheme on a two-degrees-freedom direct-drive robot manipulator

Manejo integrado costero en Cuba, la ensenada Sibarimar

The integrated managing of the zones coastal is based on the production of a plan integrated for protection and development of the ecosystems and coastal resources, trying to fulfill a few aims that are compatible with the activities that they develop and with the well-being of the communities that depend on the coastal resources.Nevertheless, some activities that exploit the resources of the coastal zones it has put in danger his sustainability, the tourism constitutes one of the activities that more has helped in the Inlet Sibarimar to put in danger this zone crust. In this article there is realized an analysis of the principal environmental problems of the area of study and there are formulated some offers that should be gathered in the production of a program of coastal managing integrated for the Inlet Sibarimar.El manejo integrado de las zonas costera se basa en la elaboración de un plan integrado para protección y desarrollo de los ecosistemas y recursos costeros, tratando de cumplir unos objetivos que sean compatibles con las actividades que desarrollan y con el bienestar de las comunidades que dependen de los recursos costeros. Sin embargo, algunas actividades que explotan los recursos de las zonas costeras ha puesto en peligro su sostenibilidad, el turismo constituye un de las actividades que más ha contribuido en la Ensenada Sibarimar a poner en peligro esta zona costera. En este artículo se realiza un análisis de los principales problemas ambientales del área de estudio y se formulan algunas propuestas que se deberían recoger en la elaboración de un programa de manejo costero integrado para la Ensenada Sibarimar.

II Seminario Internacional en Ciencias Aplicadas “Una mirada hacia la innovación y el desarrollo sostenible”

INTRODUCCIÓNLa Química, Biología y las Matemáticas son el pilar de las ciencias aplicadas. La investigación en el área básica se ve reflejada en el desarrollo de disciplinas como las ciencias de la salud, ingenierías y ciencias ambientales. De esta forma, la integración entre la investigación básica y las ciencias aplicadas es fundamental en el desarrollo del profesional moderno. Considerando lo anterior la Facultad de Ciencias Exactas Físicas y Naturales organiza el segundo seminario internacional en Ciencias Aplicadas,como una ventana a la integración de la investigación en la identificación de problemas cotidianos y a la búsqueda de soluciones a los mismos, contribuyendo a la vez el enriquecimiento profesional de los participantes y generando espacios de discusión científica en la Universidad de Santander UDES.OBJETIVOSDesarrollar temáticas de actualidad en diversas áreas del conocimiento con perspectivas de innovación y desarrollo tecnológico en áreas de la salud, investigación y el ambiente. Ofrecer talleres formativos para contextualizar el conocimiento de manera que los asistentes reconozcan las herramientas tecnológicas utilizadas para obtener mejores resultados en su futuro desempeño como profesionales

Anomalous codeposition of cobalt and ruthenium from chloride-sulfate baths

Codeposition of Ru and Co was studied at room temperature and at 50oC with various Ru3+ and Co2+ concentrations in the electrolyte. The codeposition of Co and Ru proved to be anomalous since no pure Ru could be obtained in the presence of Co2+ in the electrolyte, but a significant Co incorporation into the deposit was detected at potentials where the deposition of pure Co was not possible. The composition of the deposits varied monotonously with the change of the concentration ratio of Co2+ and Ru3+. The deposition of Ru was much hindered and the current efficiency was a few percent only when the molar fraction of Co in the deposit was low. Continuous deposits could be obtained only when the molar fraction of Co in the deposit was at least 40 at.%. The deposit morphology was related to the molar fraction of Co in the deposit. The X-ray diffractograms are in conformity with a hexagonal close-packed alloy and indicate the formation of nanocrystalline deposits. Two-pulse plating did not lead to a multilayer but to a Co-rich alloy. Magnetoresistance of the samples decreased with increasing Ru content

A specification-based QoS-aware design framework for service-based applications

Effective and accurate service discovery and composition rely on complete specifications of service behaviour, containing inputs and preconditions that are required before service execution, outputs, effects and ramifications of a successful execution and explanations for unsuccessful executions. The previously defined Web Service Specification Language (WSSL) relies on the fluent calculus formalism to produce such rich specifications for atomic and composite services. In this work, we propose further extensions that focus on the specification of QoS profiles, as well as partially observable service states. Additionally, a design framework for service-based applications is implemented based on WSSL, advancing state of the art by being the first service framework to simultaneously provide several desirable capabilities, such as supporting ramifications and partial observability, as well as non-determinism in composition schemas using heuristic encodings; providing explanations for unexpected behaviour; and QoS-awareness through goal-based techniques. These capabilities are illustrated through a comparative evaluation against prominent state-of-the-art approaches based on a typical SBA design scenario

Taxonomic and functional metagenomic profiling of the microbial community in the anoxic sediment of a sub-saline Shallow Lake (Laguna de Carrizo, Central Spain)

The phylogenetic and functional structure of the microbial community residing in a Ca2+-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO4 × 2 H2O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1 Mb of consensus metagenome sequence. The lake has about half the salinity of seawater and possesses an unusual relative concentration of ions, with Ca2+ and SO 4 2- being dominant. The 16S rRNA sequences revealed a diverse community with about 22% of the bacterial rRNAs being less than 94.5% similar to any rRNA currently deposited in GenBank. In addition to this, about 79% of the archaeal rRNA genes were mostly related to uncultured Euryarchaeota of the CCA47 group, which are often associated with marine and oxygen-depleted sites. Sequence analysis of assembled genes revealed that 23% of the open reading frames of the metagenome library had no hits in the database. Among annotated genes, functions related to (thio) sulfate and (thio) sulfonate-reduction and iron-oxidation, sulfur-oxidation, denitrification, synthrophism, and phototrophic sulfur metabolism were found as predominant. Phylogenetic and biochemical analyses indicate that the inherent physical–chemical characteristics of this habitat coupled with adaptation to anthropogenic activities have resulted in a highly efficient community for the assimilation of polysulfides, sulfoxides, and organosulfonates together with nitro-, nitrile-, and cyanide-substituted compounds. We discuss that the relevant microbial composition and metabolic capacities at Laguna de Carrizo, likely developed as an adaptation to thrive in the presence of moderate salinity conditions and potential toxic bio-molecules, in contrast with the properties of previously known anoxic sediments of shallow lakes.This research was supported by the Spanish CSD2007-00005 project and FEDER funds. M-E.G. thanks the CSIC for a JAE fellowship.Peer Reviewe

Carcass conformation and fat cover scores in beef cattle: A comparison of threshold linear models vs grouped data models

Background: Beef carcass conformation and fat cover scores are measured by subjective grading performed by trained technicians. The discrete nature of these scores is taken into account in genetic evaluations using a threshold model, which assumes an underlying continuous distribution called liability that can be modelled by different methods. Methods: Five threshold models were compared in this study: three threshold linear models, one including slaughterhouse and sex effects, along with other systematic effects, with homogeneous thresholds and two extensions with heterogeneous thresholds that vary across slaughterhouses and across slaughterhouse and sex and a generalised linear model with reverse extreme value errors. For this last model, the underlying variable followed a Weibull distribution and was both a log-linear model and a grouped data model. The fifth model was an extension of grouped data models with score-dependent effects in order to allow for heterogeneous thresholds that vary across slaughterhouse and sex. Goodness-of-fit of these models was tested using the bootstrap methodology. Field data included 2,539 carcasses of the Bruna dels Pirineus beef cattle breed. Results: Differences in carcass conformation and fat cover scores among slaughterhouses could not be totally captured by a systematic slaughterhouse effect, as fitted in the threshold linear model with homogeneous thresholds, and different thresholds per slaughterhouse were estimated using a slaughterhouse-specific threshold model. This model fixed most of the deficiencies when stratification by slaughterhouse was done, but it still failed to correctly fit frequencies stratified by sex, especially for fat cover, as 5 of the 8 current percentages were not included within the bootstrap interval. This indicates that scoring varied with sex and a specific sex per slaughterhouse threshold linear model should be used in order to guarantee the goodness-of-fit of the genetic evaluation model. This was also observed in grouped data models that avoided fitting deficiencies when slaughterhouse and sex effects were score-dependent. Conclusions: Both threshold linear models and grouped data models can guarantee the goodness-of-fit of the genetic evaluation for carcass conformation and fat cover, but our results highlight the need for specific thresholds by sex and slaughterhouse in order to avoid fitting deficiencies