Scalable Inference of Gene Regulatory Networks with the Spark Distributed Computing Platform Cristo

Inference of Gene Regulatory Networks (GRNs) remains an important open challenge in computational biology. The goal of bio-model inference is to, based on time-series of gene expression data, obtain the sparse topological structure and the parameters that quantitatively understand and reproduce the dynamics of biological system. Nevertheless, the inference of a GRN is a complex optimization problem that involve processing S-System models, which include large amount of gene expression data from hundreds (even thousands) of genes in multiple time-series (essays). This complexity, along with the amount of data managed, make the inference of GRNs to be a computationally expensive task. Therefore, the genera- tion of parallel algorithmic proposals that operate efficiently on distributed processing platforms is a must in current reconstruction of GRNs. In this paper, a parallel multi-objective approach is proposed for the optimal inference of GRNs, since min- imizing the Mean Squared Error using S-System model and Topology Regularization value. A flexible and robust multi-objective cellular evolutionary algorithm is adapted to deploy parallel tasks, in form of Spark jobs. The proposed approach has been developed using the framework jMetal, so in order to perform parallel computation, we use Spark on a cluster of distributed nodes to evaluate candidate solutions modeling the interactions of genes in biological networks.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Low-Thrust Control Strategies for Earth-to-Mars Trajectories

Recent advances in electric propulsion systems have demonstrated that these engines have the potential to be used for long-duration travels, with applications such as cargo and human transportation for interplanetary voyages. The Variable Specific Impulse Magnetoplasma Rocket (VASIMR) is an example of this type of engine, possessing the ability to operate at a wide range of specific impulse levels. This chapter presents the results of a study comparing three different thrust control strategies for Earth-Mars trajectories, using the VASIMR engine at a power of 150 kW. These are constant thrust trajectories, trajectories with coasting periods, and trajectories with variable specific impulse, resulting in variable thrust. To achieve this, an optimization tool was created using spherical coordinates to model the dynamics of the spacecraft, optimal control theory to setup the optimization problem, and a differential evolution algorithm to minimize the cost function. A novel approach to model variable specific impulse and coast-arcs in the trajectories for spherical coordinates is presented as well. The optimization tool was utilized to find optimal trajectories from Earth to Mars orbit, and it was concluded that using variable thrust reduces propellant consumption for a variety of trajectories, when compared to the other two methods

Collective effects in ultracold neutral plasmas

This thesis describes the measurements of collective effects in strongly coupled ultra-cold neutral plasmas (UNPs). It shows the implementation of experimental techniques that perturb either the density or velocity distribution of the plasma and it describes the subsequent excitation, observation and analysis of the aforementioned collective phenomena. UNPs are interesting in that they display physics of strongly coupled systems. For most plasma systems, collective effects are well described with classical hydrodynamic or kinetic descriptions. However, for strongly coupled systems, the Coulomb interaction energy between nearest neighbors exceeds the kinetic energy, and these descriptions must be modified as the plasma crosses over from a gas-like to liquid-like behavior. Strongly coupling can be found in exotic plasma systems found astrophysics, dusty plasmas, non-neutral trapped ion plasmas, intense-laser/matter interactions and inertial confinement fusion experiments. Compared to other strongly coupled plasmas, UNPs are ideal for studying collective effects in this regime since they have lower timescales, precisely controllable initial conditions and non-invasive diagnostics. Previous studies of UNPs concentrated on plasma expansion dynamics and some collective effects such as disorder induced heating, but little work had been done in relaxation or collision rates and collective modes in UNPs. This thesis presents a method for measuring collision rates by perturbing the velocity distribution of the plasma, observing plasma relaxation and measuring the relaxation rate. It also presents a new technique for observing collective modes in the plasma by perturbing the initial density of the plasma and how this results in the excitation of ion acoustic waves and a measurement of its dispersion relation. Finally, this thesis presents how this last technique can be used to create a gap in the center of the plasma and how this leads to hole propagation and plasma streaming and presents a characterization of both phenomena. The result of these experiments will be valuable for predicting the behavior of collective effects in other strongly coupled plasmas and for comparison with theories that describe them

Generación de burbujas y análisis del mezclado en columnas de flujo oscilatorio

Los reactores de flujo oscilatorio (OBR) son equipos tubulares aptos para el mezclado intensivo, en los que se superpone un flujo neto y un flujo oscilatorio. La velocidad del flujo neto que atraviesa el tubo es propia de un flujo laminar con muy bajo número de Reynolds, mientras que las velocidades superpuestas por la oscilación de tipo sinusoidal pueden ser de hasta tres órdenes de magnitud mayor. Los tubos contienen elementos insertados que promueven el mezclado radial -típicamente coronas circulares- y que proporcionan características de flujo pistón (plug flow) a la vez que se alcanzan tiempos de residencia muy altos. En numerosas reacciones químicas se mezclan reactivos líquidos y gaseosos, junto con catalizadores sólidos, como es el caso de los procesos de hidrogenación. El mezclado del líquido y gas es fundamental para conseguir una reacción corta y sin productos secundarios. En este proyecto se acomete la modelización del flujo líquido-gas en estas columnas, con el objetivo de poder evaluar las características de difusión y mezclado.Escuela Técnica Superior de Ingeniería IndustrialUniversidad Politécnica de Cartagen

A New Multi-Objective Approach for Molecular Docking Based on RMSD and Binding Energy

Ligand-protein docking is an optimization problem based on predicting the position of a ligand with the lowest binding energy in the active site of the receptor. Molecular docking problems are traditionally tackled with single-objective, as well as with multi-objective approaches, to minimize the binding energy. In this paper, we propose a novel multi-objective formulation that considers: the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands and the binding (intermolecular) energy, as two objectives to evaluate the quality of the ligand-protein interactions. To determine the kind of Pareto front approximations that can be obtained, we have selected a set of representative multi-objective algorithms such as NSGA-II, SMPSO, GDE3, and MOEA/D. Their performances have been assessed by applying two main quality indicators intended to measure convergence and diversity of the fronts. In addition, a comparison with LGA, a reference single-objective evolutionary algorithm for molecular docking (AutoDock) is carried out. In general, SMPSO shows the best overall results in terms of energy and RMSD (value lower than 2A for successful docking results). This new multi-objective approach shows an improvement over the ligand-protein docking predictions that could be promising in in silico docking studies to select new anticancer compounds for therapeutic targets that are multidrug resistant.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Percolation on patchwise heterogeneous surfaces under equilibrium conditions

The site percolation problem on square lattices whose sites are grouped in two types of energetically different patches is studied. Several lattices formed by collections of either randomly or orderly localized and no overlapped patches of different sizes are generated. The system is characterized by two parameters, namely, the size of each patch, l, and the energy difference between the two kind of sites, E. Particles are adsorbed at equilibrium on the lattice. The critical coverage is determined by means of Monte Carlo simulations and finite-size scaling analysis. The percolative behavior of the system as a function of the parameters characterizing the heterogeneity of the energetic surface topography is presented and discussed.Fil: Gimenez, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Ramirez Pastor, Antonio Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Nieto Quintas, Felix Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentin

Percolation of interacting particles on heterogenous surfaces

The percolation problem of interacting particles on square lattices with two kinds of energetically different sites is studied. Square lattices formed by collections of either randomly or orderly distributed sites are generated. The system is characterized by two parameters, namely, the interaction between adjacent particles, ω, and the energy difference between the two kinds of sites, 1E. Particles are adsorbed at equilibrium on the lattice. By means of Monte Carlo simulations and finite-size scaling analysis the critical coverage is determined. The percolative behavior of the system is presented and discussed in terms of the mentioned parameters, ω and 1E.Fil: Giménez, María Cecilia. Universidad Nacional de San Luis; ArgentinaFil: Ramirez Pastor, Antonio Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Nieto Quintas, Felix Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentin

Novel order parameter to describe the critical behavior of Ising spin glass models

A novel order parameter Φ for spin glasses is defined based on topological criteria and with a clear physical interpretation. Φ is first investigated for well known magnetic systems and then applied to the Edwards-Anderson ±J model on a square lattice, comparing its properties with the usual q order parameter. Finite size scaling procedures are performed. Results and analyses based on Φ confirm a zero temperature phase transition and allow to identify the low temperature phase. The advantages of Φ are brought out and its physical meaning is established.Fil: Romá, Federico José. Universidad Nacional de San Luis; ArgentinaFil: Nieto Quintas, Felix Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Ramirez Pastor, Antonio Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Vogel, E. E.. Universidad de La Frontera; Chil

Lattice-gas model of nonadditive interacting particles on nanotubes bundles

In the present paper, the adsorption thermodynamics of a lattice-gas model which mimics a nanoporous environment is studied by considering nonadditive interactions between the adsorbed particles. It is assumed that the energy linking a certain atom with any of its nearest neighbors strongly depends on the state of occupancy in the first coordination sphere of such an adatom. By means of Monte Carlo (MC) simulations in the grand canonical ensemble, adsorption isotherms and differential heats of adsorption were calculated. Their striking behaviors were analyzed and discussed in terms of the low temperature phases formed in the system. Finally, the results obtained from MC simulations were compared with the corresponding ones from Bragg–Williams approximation.Fil: Pinto, Oscar Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Pasinetti, Pedro Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Nieto Quintas, Felix Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; ArgentinaFil: Ramirez Pastor, Antonio Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich". Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto de Física Aplicada "Dr. Jorge Andrés Zgrablich"; Argentin

Nuevas citas de macrófitos acuáticos de las zonas húmedas de la provincia de Málaga

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