Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Generality and legibility in mobile manipulation

This article investigates methods for achieving more general manipulation capabilities for mobile manipulation platforms, which produce legible behavior in human living environments. To achieve generality and legibility, we combine two control mechanisms. First of all, experience- and observation-based learning of skills is applied to routine tasks, so that the repetitive and stereotypical character of everyday activity is exploited. Second, we use planning, reasoning, and search for novel tasks which have no stereotypical solution. We apply these ideas to the learning and use of action-related places, to the model-based visual recognition and localization of objects, and the learning and application of reaching strategies and motions from humans. We demonstrate the integration of these mechanisms into a single low-level control system for autonomous manipulation platforms.     

Projective active shape models for pose-variant image analysis of quasi-planar objects: Application to facial analysis

One of the important obstacles in the image-based analysis of the human face is the 3D nature of the problem and the 2D nature of most imaging systems used for biometric applications. Due to this, accuracy is strongly influenced by the viewpoint of the images, being frontal views the most thoroughly studied. However, when fully automatic face analysis systems are designed, capturing frontal-view images cannot be guaranteed. Examples of this situation can be found in surveillance systems, car driver images or whenever there are architectural constraints that prevent from placing a camera frontal to the subject. Taking advantage of the fact that most facial features lie approximately on the same plane, we propose the use of projective geometry across different views. An active shape model constructed with frontal-view images can then be directly applied to the segmentation of pictures taken from other viewpoints. The proposed extension demonstrates being significantly more invariant than the standard approach. Validation of the method is presented in 360 images from the AV@CAR database, systematically divided into three different rotations (to both sides), as well as upper and lower views due to nodding. The presented tests are among the largest quantitative results reported to date in face segmentation under varying poses.     

A complete and efficient CUDA-sharing solution for HPC clusters

In this paper we detail the key features, architectural design, and implementation of rCUDA, an advanced framework to enable remote and transparent GPGPU acceleration in HPC clusters. rCUDA allows decoupling GPUs from nodes, forming pools of shared accelerators, which brings enhanced flexibility to cluster configurations. This opens the door to configurations with fewer accelerators than nodes, as well as permits a single node to exploit the whole set of GPUs installed in the cluster. In our proposal, CUDA applications can seamlessly interact with any GPU in the cluster, independently of its physical location. Thus, GPUs can be either distributed among compute nodes or concentrated in dedicated GPGPU servers, depending on the cluster administrator’s policy. This proposal leads to savings not only in space but also in energy, acquisition, and maintenance costs. The performance evaluation in this paper with a series of benchmarks and a production application clearly demonstrates the viability of this proposal. Concretely, experiments with the matrix–matrix product reveal excellent performance compared with regular executions on the local GPU; on a much more complex application, the GPU-accelerated LAMMPS, we attain up to 11x speedup employing 8 remote accelerators from a single node with respect to a 12-core CPU-only execution. GPGPU service interaction in compute nodes, remote acceleration in dedicated GPGPU servers, and data transfer performance of similar GPU virtualization frameworks are also evaluated.     

Ontological reasoning for improving the treatment of emotions in text

With the advent of affective computing, the task of adequately identifying, representing and processing the emotional connotations of text has acquired importance. Two problems facing this task are addressed in this paper: the composition of sentence emotion from word emotion, and a representation of emotion that allows easy conversion between existing computational representations. The emotion of a sentence of text should be derived by composition of the emotions of the words in the sentence, but no method has been proposed so far to model this compositionality. Of the various existing approaches for representing emotions, some are better suited for some problems and some for others, but there is no easy way of converting from one to another. This paper presents a system that addresses these two problems by reasoning with two ontologies implemented with Semantic Web technologies: one designed to represent word dependency relations within a sentence, and one designed to represent emotions. The ontology of word dependency relies on roles to represent the way emotional contributions project over word dependencies. By applying automated classification of mark-up results in terms of the emotion ontology the system can interpret unrestricted input in terms of a restricted set of concepts for which particular rules are provided. The rules applied at the end of the process provide configuration parameters for a system for emotional voice synthesis.     

Model-driven engineering for mobile robotic systems: a systematic mapping study

Software and Systems Modeling - Mobile robots operate in various environments (e.g. aquatic, aerial, or terrestrial), they come in many diverse shapes and they are increasingly becoming parts of...     

DCOP FOR SMART HOMES: A CASE STUDY

The aim of this article is to bring forth the issue of integrating the services provided by intelligent artifacts in Ambient Intelligence applications. Specifically, we propose a Distributed Constraint Optimization procedure for achieving a functional integration of intelligent artifacts in a smart home. To this end, we employ Adopt-N , a state-of-the-art algorithm for solving Distributed Constraint Optimization Problems (DCOP). This article attempts to state the smart home coordination problem in general terms, and provides the details of a DCOP-based approach by describing a case study taken from the RoboCare project. More specifically, we show how (1) DCOP is a convenient metaphor for casting smart home coordination problems, and (2) the specific features which distinguish Adopt-N from other algorithms for DCOP represent a strong asset in the smart home domain.     

Subspace identification of MIMO LPV systems using a periodic scheduling sequence

A novel subspace identification method is presented which is able to reconstruct the deterministic part of a multivariable state-space LPV system with affine parameter dependence, in the presence of process and output noise. It is assumed that the identification data is generated with the scheduling variable varying periodically during the course of the identification experiment. This allows to use methods from LTI subspace identification to determine the column space of the time-varying observability matrices. It is shown that the crucial step in determining the original LPV system is to ensure the obtained observability matrices are defined with respect to the same state basis. Once the LPV model has been identified, it is valid for other nonperiodic scheduling sequences as well.     

Nogood-FC for solving partitionable constraint satisfaction problems

Many real problems can be naturally modelled as constraint satisfaction problems (CSPs). However, some of these problems are of a distributed nature, which requires problems of this kind to be modelled as distributed constraint satisfaction problems (DCSPs). In this work, we present a distributed model for solving CSPs. Our technique carries out a partition over the constraint network using a graph partitioning software; after partitioning, each sub-CSP is arranged into a DFS-tree CSP structure that is used as a hierarchy of communication by our distributed algorithm. We show that our distributed algorithm outperforms well-known centralized algorithms solving partitionable CSPs.     

Influences of data filtering on human–computer interaction by gaze-contingent display and eye-tracking applications

We describe an interactive gaze-contingent display (GCD) applied to clinical applications; the system uses a simple texture hole to inhibit peripheral vision, to test and stress overt mechanisms of visual searching in normal subjects. The correct use of GCD in vision research is affected by tremor of the hole, due to system noise, nystagmus, eye blinking, calibration and subject reactivity. These issues compromise the execution of task. In order to obtain a stable GCD hole, we implemented a predictive gaze-contingent display (PGCD), fitting through dispersion of fixations and modulating a filter. The paper describes the PGCD and compare it with the common technique, providing evidence that humans fit exploration based on the characteristics of the computer system; in particular we found significant difference applying PGCD or a simple finite impulse response filter. We suggest that a correct human–computer interaction applied to neuropsychological context must be developed taking in consideration both technical point of view and human behavior.