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.

The theory of complexity adapted to international relations: the behaviour of the visegrad-ukraine complex adaptive system since November 2013

La teoría de la complejidad, propia del estudio de fenómenos relativos a las ciencias naturales, se muestra como un marco alternativo para comprender los eventos emergentes que surgen en el sistema internacional. Esta monografía correlaciona el lenguaje de la complejidad con las relaciones internacionales, enfocándose en la relación Visegrad—Ucrania, ya que ha sido escenario de una serie de eventos emergentes e inesperados desde las protestas civiles de noviembre de 2013 en Kiev. El sistema complejo que existe entre el Grupo Visegrad y Ucrania se ve , desde entonces, en la necesidad de adaptarse ante los recurrentes eventos emergentes y de auto organizarse. De ese modo, podrá comportarse en concordancia con escenarios impredecibles, particularmente en lo relacionado con sus interacciones energéticas y sus interconexiones políticas.

Las Imágenes del malestar. Representaciones del yo y la construcción de subjetividad en la producción audiovisual contemporánea y en los nuevos dispositivos tecnológicos

El tema de la investigación propuesto aquí, se centra en el malestar social, y la representación de éste desde un punto de vista personal y autobiográfico, algo que en estas página denomino Autorepresentación del malestar social. ¿Cómo se autorepresenta el malestar y qué prácticas artísticas se emplean para ello? ¿Cuáles son la transformaciones que provocan estas prácticas artísticas en el terreno audiovisual? En este sentido, exploraremos dos vías de análisis: por un lado nos interesa observar cuales han sido las modificaciones que el poder ha desarrollado para establecer nuevas formas de explotación, y por otro lado, veremos como estas modificaciones están generando una nueva praxis social donde las prácticas artísticas cobran un nuevo y reforzado sentido, así como una nueva capacidad política, individual y colectiva a un mismo tiempo, cargada de una fuerza transformadora capaz de componer nuevos espacios de sujeto. Analizaremos, desde la representación del yo en la vida cotidiana, el género y las relaciones interpersonales, hasta las transformaciones contemporáneas del trabajo, y los cambios en la construcción de la subjetividad. El principal elemento en el que se apoyaran nuestras investigaciones será el anàlisis de producciones audiovisuales contemporáneas y la distribución de estas en algunas de las redes de comunicación contemporáneas, intentando mostrar, de esta manera, la interacción y los efectos directos que provocan en la realidad social.

Microcrédito e empoderamento de mulheres de baixa renda: uma análise do projeto “elas”

O microcrédito tem sido uma ferramenta de combate à pobreza no mundo todo nas últimas décadas. A ampliação do acesso ao crédito àqueles que não podem recorrer ao sistema financeiro tradicional tem se constituído como uma via democrática de fomento à inclusão social através da geração de trabalho e renda. Os empréstimos realizados têm demonstrado efeitos benéficos sobre a comunidades de baixa renda, especialmente em relação às mulheres, pelo desencadeamento de um processo de empoderamento com efeitos em sua capacidade de auferir renda, melhorar sua autoestima e ampliar sua participação em espaços de tomada de decisão. No Brasil, as mulheres são a maioria dos tomadores de microcrédito e a justificativa para isso perpassa pelas dificuldades relativas ao mercado formal, a necessidade de complementação da renda familiar, o desejo de maior emancipação frente aos companheiros e a busca pela realização num pequeno empreendimento próprio. Em Fortaleza (CE), o Banco Palmas criou um projeto de empoderamento de gênero, focado em beneficiárias do Programa Bolsa Família, a partir da concessão de microcrédito. A presente dissertação teve como objetivo analisar as dimensões do processo de empoderamento alcançadas pelas mulheres participantes deste projeto, intitulado como projeto “ELAS”. A hipótese inicial era a de que a nova capacidade economicamente produtiva das entrevistadas modificaria sua realidade, colocando-as em um novo patamar frente a si mesmas e às suas famílias, proporcionando maior autonomia em suas decisões de consumo e independência financeira frente a seus maridos, além do aumento de seu bem-estar. Nesse caso, o microcrédito serviria como um fomentador do empoderamento individual feminino, hipótese comprovada neste estudo. Entretanto, notou-se que não houve um rompimento das relações de gênero no âmbito das famílias, fator perceptível principalmente pela não redistribuição das tarefas domiciliares, com impactos restritivos no empoderamento social dessas mulheres através da não participação em instâncias coletivas de tomada de decisão.

Centro da atividade modelo centro-dia do idoso no município de Presidente Prudente

This final work graduation presents a proposal model Seniors Center Day in the city of Presidente Prudente. The municipality has local (private and public) with socialization activities and some medical treatments for the elderly, but the attendance capacity is not sufficient and in some places the infrastructure is not adequate, as in Case Study Centro de Referência do Idoso Feliz Idade maintained by Presidente Prudente Prefecture. From projective references created the model Centro da Atividade that integrates users in the city through the spatial continuity (main architectural party) and physical and psychological comfort of the elderly. The space designed has strong links with the external environment, creating relationships of older people with nature through living spaces to free up and the psychological comfort (and the relation with nature) is present in the project through spaces with elements that make part of the affective memory of users

A tuple space implementation for large-scale infrastructures

Coordinating activities in a distributed system is an open research topic. Several models have been proposed to achieve this purpose such as message passing, publish/subscribe, workflows or tuple spaces. We have focused on the latter model, trying to overcome some of its disadvantages. In particular we have applied spatial database techniques to tuple spaces in order to increase their performance when handling a large number of tuples. Moreover, we have studied how structured peer to peer approaches can be applied to better distribute tuples on large networks. Using some of these result, we have developed a tuple space implementation for the Globus Toolkit that can be used by Grid applications as a coordination service. The development of such a service has been quite challenging due to the limitations imposed by XML serialization that have heavily influenced its design. Nevertheless, we were able to complete its implementation and use it to implement two different types of test applications: a completely parallelizable one and a plasma simulation that is not completely parallelizable. Using this last application we have compared the performance of our service against MPI. Finally, we have developed and tested a simple workflow in order to show the versatility of our service.

Territorialidades, espacios vividos y sentidos de lugar en tiempos de avance de la frontera productiva

En pleno proceso de corrimiento de la frontera productiva y emergente disputa por el uso y apropiación de los recursos, la intervención de distintos sujetos sociales en el oeste de La Pampa está redefiniendo las prácticas productivas-reproductivas de los crianceros campesinos y, en consecuencia, la construcción social del espacio. Desde la finalización de las campañas militares contra las sociedades indígenas diferentes agentes, mediante el ejercicio de poder, construyeron determinadas representaciones territoriales y pusieron en acción prácticas tendientes a articular el oeste pampeano con la economía nacional. Sin embargo la escasa valorización de este espacio posibilitó el desarrollo de cierta autonomía en las formas de organización socio-productivas y simbólicas. Ante la expansión de la frontera ganadera, el impuso hidrocarburífero en la región y creciente presencia de nuevas lógicas territoriales crecen las confrontaciones por el desigual acceso a los recursos naturales, por la apropiación del espacio y la construcción de territorialidades. En este marco, el artículo focaliza la mirada en la organización interna de los asentamientos rurales y en los usos sociales de los espacios a través del tiempo, en dos áreas del "extremo" oeste: La Humada y Chos Malal. De este modo se pretende establecer cómo se organizaron diacrónicamente los espacios doméstico, peridoméstico y monte y qué sentidos expresan los sujetos en torno a los espacios de vida y lugares en tiempos de expansión de la frontera productiva. El nuevo campo social generado producto del avance del capitalismo sobre las unidades campesinas se expresa, no sólo en las modificaciones en las formas de manejo del ganado, organización de la producción y construcción social del espacio, sino también en las formas de sociabilidad y estrategias de resistencia colectivas. Este proceso, que se está gestando en la región, tiene un desarrollo similar en otros espacios donde el avance productivo se ha generado con anterioridad o a un ritmo más acelerado. Para la realización de la investigación se articulan diferentes estrategias de metodología cualitativa que combinan el estudio de caso con historias de vida, entrevistas en profundidad y análisis de fuentes documentales.

Territorialidades, espacios vividos y sentidos de lugar en tiempos de avance de la frontera productiva

En pleno proceso de corrimiento de la frontera productiva y emergente disputa por el uso y apropiación de los recursos, la intervención de distintos sujetos sociales en el oeste de La Pampa está redefiniendo las prácticas productivas-reproductivas de los crianceros campesinos y, en consecuencia, la construcción social del espacio. Desde la finalización de las campañas militares contra las sociedades indígenas diferentes agentes, mediante el ejercicio de poder, construyeron determinadas representaciones territoriales y pusieron en acción prácticas tendientes a articular el oeste pampeano con la economía nacional. Sin embargo la escasa valorización de este espacio posibilitó el desarrollo de cierta autonomía en las formas de organización socio-productivas y simbólicas. Ante la expansión de la frontera ganadera, el impuso hidrocarburífero en la región y creciente presencia de nuevas lógicas territoriales crecen las confrontaciones por el desigual acceso a los recursos naturales, por la apropiación del espacio y la construcción de territorialidades. En este marco, el artículo focaliza la mirada en la organización interna de los asentamientos rurales y en los usos sociales de los espacios a través del tiempo, en dos áreas del "extremo" oeste: La Humada y Chos Malal. De este modo se pretende establecer cómo se organizaron diacrónicamente los espacios doméstico, peridoméstico y monte y qué sentidos expresan los sujetos en torno a los espacios de vida y lugares en tiempos de expansión de la frontera productiva. El nuevo campo social generado producto del avance del capitalismo sobre las unidades campesinas se expresa, no sólo en las modificaciones en las formas de manejo del ganado, organización de la producción y construcción social del espacio, sino también en las formas de sociabilidad y estrategias de resistencia colectivas. Este proceso, que se está gestando en la región, tiene un desarrollo similar en otros espacios donde el avance productivo se ha generado con anterioridad o a un ritmo más acelerado. Para la realización de la investigación se articulan diferentes estrategias de metodología cualitativa que combinan el estudio de caso con historias de vida, entrevistas en profundidad y análisis de fuentes documentales.

Territorialidades, espacios vividos y sentidos de lugar en tiempos de avance de la frontera productiva

En pleno proceso de corrimiento de la frontera productiva y emergente disputa por el uso y apropiación de los recursos, la intervención de distintos sujetos sociales en el oeste de La Pampa está redefiniendo las prácticas productivas-reproductivas de los crianceros campesinos y, en consecuencia, la construcción social del espacio. Desde la finalización de las campañas militares contra las sociedades indígenas diferentes agentes, mediante el ejercicio de poder, construyeron determinadas representaciones territoriales y pusieron en acción prácticas tendientes a articular el oeste pampeano con la economía nacional. Sin embargo la escasa valorización de este espacio posibilitó el desarrollo de cierta autonomía en las formas de organización socio-productivas y simbólicas. Ante la expansión de la frontera ganadera, el impuso hidrocarburífero en la región y creciente presencia de nuevas lógicas territoriales crecen las confrontaciones por el desigual acceso a los recursos naturales, por la apropiación del espacio y la construcción de territorialidades. En este marco, el artículo focaliza la mirada en la organización interna de los asentamientos rurales y en los usos sociales de los espacios a través del tiempo, en dos áreas del "extremo" oeste: La Humada y Chos Malal. De este modo se pretende establecer cómo se organizaron diacrónicamente los espacios doméstico, peridoméstico y monte y qué sentidos expresan los sujetos en torno a los espacios de vida y lugares en tiempos de expansión de la frontera productiva. El nuevo campo social generado producto del avance del capitalismo sobre las unidades campesinas se expresa, no sólo en las modificaciones en las formas de manejo del ganado, organización de la producción y construcción social del espacio, sino también en las formas de sociabilidad y estrategias de resistencia colectivas. Este proceso, que se está gestando en la región, tiene un desarrollo similar en otros espacios donde el avance productivo se ha generado con anterioridad o a un ritmo más acelerado. Para la realización de la investigación se articulan diferentes estrategias de metodología cualitativa que combinan el estudio de caso con historias de vida, entrevistas en profundidad y análisis de fuentes documentales.

Bio-inspired FPGA Architecture for Self-Calibration of an Image Compression Core based on Wavelet Transforms in Embedded Systems

A generic bio-inspired adaptive architecture for image compression suitable to be implemented in embedded systems is presented. The architecture allows the system to be tuned during its calibration phase. An evolutionary algorithm is responsible of making the system evolve towards the required performance. A prototype has been implemented in a Xilinx Virtex-5 FPGA featuring an adaptive wavelet transform core directed at improving image compression for specific types of images. An Evolution Strategy has been chosen as the search algorithm and its typical genetic operators adapted to allow for a hardware friendly implementation. HW/SW partitioning issues are also considered after a high level description of the algorithm is profiled which validates the proposed resource allocation in the device fabric. To check the robustness of the system and its adaptation capabilities, different types of images have been selected as validation patterns. A direct application of such a system is its deployment in an unknown environment during design time, letting the calibration phase adjust the system parameters so that it performs efcient image compression. Also, this prototype implementation may serve as an accelerator for the automatic design of evolved transform coefficients which are later on synthesized and implemented in a non-adaptive system in the final implementation device, whether it is a HW or SW based computing device. The architecture has been built in a modular way so that it can be easily extended to adapt other types of image processing cores. Details on this pluggable component point of view are also given in the paper.

Bio-inspired enhancement of reputation systems for intelligent environments

Providing security to the emerging field of ambient intelligence will be difficult if we rely only on existing techniques, given their dynamic and heterogeneous nature. Moreover, security demands of these systems are expected to grow, as many applications will require accurate context modeling. In this work we propose an enhancement to the reputation systems traditionally deployed for securing these systems. Different anomaly detectors are combined using the immunological paradigm to optimize reputation system performance in response to evolving security requirements. As an example, the experiments show how a combination of detectors based on unsupervised techniques (self-organizing maps and genetic algorithms) can help to significantly reduce the global response time of the reputation system. The proposed solution offers many benefits: scalability, fast response to adversarial activities, ability to detect unknown attacks, high adaptability, and high ability in detecting and confining attacks. For these reasons, we believe that our solution is capable of coping with the dynamism of ambient intelligence systems and the growing requirements of security demands.

BIO-INSPIRED COMPUTATIONAL TECHNIQUES APPLIED TO THE CLUSTERING AND VISUALIZATION OF SPATIO-TEMPORAL GEOSPATIAL DATA

The coverage and volume of geo-referenced datasets are extensive and incessantly¦growing. The systematic capture of geo-referenced information generates large volumes¦of spatio-temporal data to be analyzed. Clustering and visualization play a key¦role in the exploratory data analysis and the extraction of knowledge embedded in¦these data. However, new challenges in visualization and clustering are posed when¦dealing with the special characteristics of this data. For instance, its complex structures,¦large quantity of samples, variables involved in a temporal context, high dimensionality¦and large variability in cluster shapes.¦The central aim of my thesis is to propose new algorithms and methodologies for¦clustering and visualization, in order to assist the knowledge extraction from spatiotemporal¦geo-referenced data, thus improving making decision processes.¦I present two original algorithms, one for clustering: the Fuzzy Growing Hierarchical¦Self-Organizing Networks (FGHSON), and the second for exploratory visual data analysis:¦the Tree-structured Self-organizing Maps Component Planes. In addition, I present¦methodologies that combined with FGHSON and the Tree-structured SOM Component¦Planes allow the integration of space and time seamlessly and simultaneously in¦order to extract knowledge embedded in a temporal context.¦The originality of the FGHSON lies in its capability to reflect the underlying structure¦of a dataset in a hierarchical fuzzy way. A hierarchical fuzzy representation of¦clusters is crucial when data include complex structures with large variability of cluster¦shapes, variances, densities and number of clusters. The most important characteristics¦of the FGHSON include: (1) It does not require an a-priori setup of the number¦of clusters. (2) The algorithm executes several self-organizing processes in parallel.¦Hence, when dealing with large datasets the processes can be distributed reducing the¦computational cost. (3) Only three parameters are necessary to set up the algorithm.¦In the case of the Tree-structured SOM Component Planes, the novelty of this algorithm¦lies in its ability to create a structure that allows the visual exploratory data analysis¦of large high-dimensional datasets. This algorithm creates a hierarchical structure¦of Self-Organizing Map Component Planes, arranging similar variables' projections in¦the same branches of the tree. Hence, similarities on variables' behavior can be easily¦detected (e.g. local correlations, maximal and minimal values and outliers).¦Both FGHSON and the Tree-structured SOM Component Planes were applied in¦several agroecological problems proving to be very efficient in the exploratory analysis¦and clustering of spatio-temporal datasets.¦In this thesis I also tested three soft competitive learning algorithms. Two of them¦well-known non supervised soft competitive algorithms, namely the Self-Organizing¦Maps (SOMs) and the Growing Hierarchical Self-Organizing Maps (GHSOMs); and the¦third was our original contribution, the FGHSON. Although the algorithms presented¦here have been used in several areas, to my knowledge there is not any work applying¦and comparing the performance of those techniques when dealing with spatiotemporal¦geospatial data, as it is presented in this thesis.¦I propose original methodologies to explore spatio-temporal geo-referenced datasets¦through time. Our approach uses time windows to capture temporal similarities and¦variations by using the FGHSON clustering algorithm. The developed methodologies¦are used in two case studies. In the first, the objective was to find similar agroecozones¦through time and in the second one it was to find similar environmental patterns¦shifted in time.¦Several results presented in this thesis have led to new contributions to agroecological¦knowledge, for instance, in sugar cane, and blackberry production.¦Finally, in the framework of this thesis we developed several software tools: (1)¦a Matlab toolbox that implements the FGHSON algorithm, and (2) a program called¦BIS (Bio-inspired Identification of Similar agroecozones) an interactive graphical user¦interface tool which integrates the FGHSON algorithm with Google Earth in order to¦show zones with similar agroecological characteristics.

Bio-inspired optimization & sampling technique for side-chain packing in MCCE

The prediction of proteins' conformation helps to understand their exhibited functions, allows for modeling and allows for the possible synthesis of the studied protein. Our research is focused on a sub-problem of protein folding known as side-chain packing. Its computational complexity has been proven to be NP-Hard. The motivation behind our study is to offer the scientific community a means to obtain faster conformation approximations for small to large proteins over currently available methods. As the size of proteins increases, current techniques become unusable due to the exponential nature of the problem. We investigated the capabilities of a hybrid genetic algorithm / simulated annealing technique to predict the low-energy conformational states of various sized proteins and to generate statistical distributions of the studied proteins' molecular ensemble for pKa predictions. Our algorithm produced errors to experimental results within .acceptable margins and offered considerable speed up depending on the protein and on the rotameric states' resolution used.

ORGANOSILICON BIOTECHNOLOGY: A BIO-INSPIRED APPROACH TO THE HYDROLYSIS OF ALKOXYSILANES and THE LIPASE-CATALYZED SYNTHESIS OF SILOXANE-CONTAINING POLYESTERS AND POLYAMIDES

The first part of this thesis studied the capacity of amino acids and enzymes to catalyze the hydrolysis and condensation of tetraethoxysilane and phenyltrimethoxysilane. Selected amino acids were shown to accelerate the hydrolysis and condensation of tetraethoxysilane under ambient temperature, pressure and at neutral pH (pH 7±0.02). The nature of the side chain of the amino acid was important in promoting hydrolysis and condensation. Several proteases were shown to have a capacity to hydrolyze tri- and tet-ra- alkoxysilanes under the same mild reaction conditions. The second part of this thesis employed an immobilized Candida antarctica lipase B (Novozym-435, N435) to produce siloxane-containing polyesters, polyamides, and polyester amides under solvent-free conditions. Enzymatic activity was shown to be temperature dependent, increasing until enzyme denaturation became the dominant pro-cess, which typically occurred between 120-130ᵒC. The residual activity of N435 was, on average, greater than 90%, when used in the synthesis of disiloxane-containing polyesters, regardless of the polymerization temperature except at the very highest temperatures, 140-150ᵒC. A study of the thermal tolerance of N435 determined that, over ten reaction cycles, there was a decrease in the initial rate of polymerization with each consecutive use of the catalyst. No change in the degree of monomer conversion after a 24 hour reaction cycle was found.