Computational Study of the Fe(CN)(2)CO Cofactor and Its Binding to HypC Protein.

In the intricate maturation process of [NiFe]-hydrogenases, the Fe(CN)2CO cofactor is first assembled in a HypCD complex with iron coordinated by cysteines from both proteins and CO is added after ligation of cyanides. The small accessory protein HypC is known to play a role in delivering the cofactor needed for assembling the hydrogenase active site. However, the chemical nature of the Fe(CN)2CO moiety and the stability of the cofactor–HypC complex are open questions. In this work, we address geometries, properties, and the nature of bonding of all chemical species involved in formation and binding of the cofactor by means of quantum calculations. We also study the influence of environmental effects and binding to cysteines on vibrational frequencies of stretching modes of CO and CN used to detect the presence of Fe(CN)2CO. Carbon monoxide is found to be much more sensitive to sulfur binding and the polarity of the medium than cyanides. The stability of the HypC–cofactor complex is analyzed by means of molecular dynamics simulation of cofactor-free and cofactor-bound forms of HypC. The results show that HypC is stable enough to carry the cofactor, but since its binding cysteine is located at the N-terminal unstructured tail, it presents large motions in solution, which suggests the need for a guiding interaction to achieve delivery of the cofactor.

Simulation of the deformation of polycrystalline nanostructured Ti by computational homogenization

Computational homogenization by means of the finite element analysis of a representative volume element of the microstructure is used to simulate the deformation of nanostructured Ti. The behavior of each grain is taken into account using a single crystal elasto-viscoplastic model which includes the microscopic mechanisms of plastic deformation by slip along basal, prismatic and pyramidal systems. Two different representations of the polycrystal were used. Each grain was modeled with one cubic finite element in the first one while many cubic elements were used to represent each grain in the second one, leading to a model which includes the effect of grain shape and size in a limited number of grains due to the computational cost. Both representations were used to simulate the tensile deformation of nanostructured Ti processed by ECAP-C as well as the drawing process of nanostructured Ti billets. It was found that the first representation based in one finite element per grain led to a stiffer response in tension and was not able to predict the texture evolution during drawing because the strain gradient within each grain could not be captured. On the contrary, the second representation of the polycrystal microstructure with many finite elements per grain was able to predict accurately the deformation of nanostructured Ti.

A contribution to appendage drag extrapolation using computational tools

In this paper, the foundations of the beta method, widely used in todays ship appendage extrapolations, are explored. The present work pretends to validate the Beta Method using experimental and computational tools. The ship used is a rounded bow tugboat with two significant appendages, namely, a midship protective structure for the propulsion system and a stern keel. The experimental and computational data was obtained through Towing Tank trials and a RANSE CFD code, respectively.

A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientic Work ows: A Case Study

Reproducible research in scientic work ows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and nal results, improves understanding, and permits replaying a work ow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We dene a process for documenting the work ow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation sing a real work ow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predened virtual machine image on both computing platforms.

Some theoretical aspects in computational analysis of adhesive lap joints

This paper is devoted to the numerical analysis of bidimensional bonded lap joints. For this purpose, the stress singularities occurring at the intersections of the adherend-adhesive interfaces with the free edges are first investigated and a method for computing both the order and the intensity factor of these singularities is described briefly. After that, a simplified model, in which the adhesive domain is reduced to a line, is derived by using an asymptotic expansion method. Then, assuming that the assembly debonding is produced by a macro-crack propagation in the adhesive, the associated energy release rate is computed. Finally, a homogenization technique is used in order to take into account a preliminary adhesive damage consisting of periodic micro-cracks. Some numerical results are presented.

Aeroacoustics in high speed trains

Este trabajo se centra en el estudio de problemas aeroacústicos en los trenes de alta velocidad. Se han considerado dos escenarios en los que las ondas de presión generadas son críticos para el confort de los pasajeros. Uno es el debido a las ondas de presión que genera el tren cuando entra y sale de un túnel, que a su vez producen saltos de presión de baja frecuencia en el tren (cuando se cruzan con él) y en los alrededores del túnel cuando alcanzan la salida. Se estudia este fenómeno, y se propone un sistema aeroelástico basado en el galope transversal para disminuir la energía de estas ondas, y se analiza la energía extraíble de las ondas utilizando cuerpos con diferentes secciones transversales [Sorribes-Palmer and Sanz-Andres, 2013]. La influencia de la geometría de los portales en la energía radiada hacia el exterior de túnel es analizada experimentalmente, prestando especial atención a las boquillas porosas. Las ondas de presión en el interior del túnel se han analizado mediante el método de las características. Se han realizado ensayos experimentales para estimar la energía reflejada hacia el interior del túnel al alcanzar las ondas de presión el portal de salida del túnel. Se ha estudiado la formación e interacción entre el portal del túnel y la onda de choque generada en los túneles de gran longitud y pequeña fricción. Se propone un método para describir de forma aproximada el ruido radiado al exterior. Por otro lado se ha estudiado el ruido de media y alta frecuencia de origen aerodinámico. Se ha estudiado la influencia del desprendimiento de la capa límite sobre el tren. Se propone una metodología basada en una sección de tren característica para predecir rápidamente el nivel de presión de sonido dentro y fuera del tren para todo el rango de frecuencias. Se han realizado medidas experimentales en vía de los espectros de presión sobre la superficie del tren, y de la transmisibilidad de las uniones entre estructura y revestimiento. Los resultados experimentales se han utilizado en los modelos vibroacústicos. El método de la sección del tren característica es especialmente útil a altas frecuencias cuando todo el tren se puede modelar mediante el ensamblaje de diferentes secciones características utilizando el análisis estadístico de la energía. ABSTRACT This work is focused on the study of aeroacoustic problems in high speed trains. We have considered two scenarios in which the pressure waves generated are critical for passengers comfort. The first one is due to the pressure waves generated by a train entering in a tunnel. These waves generate pressure gauges inside the train (when they find each other) and outside of the tunnel portals. This phenomenon has been studied, and an aeroelastic system based on transverse galloping to reduce the energy of these waves is proposed. The maximum extractable energy by using bodies with different cross-section shapes is analyzed. The influence of the portals geometry in the energy radiated outwards the tunnel is analyzed experimentally, with particular attention to the porous exits. The pressure waves inside the tunnel have been analyzed using the method of characteristics. Experimental tests to estimate the energy reflected into the tunnel when the pressure waves reach the tunnel portal have been performed. We have studied the generation and interaction between the tunnel portal and a shock wave generated in long tunnels with small friction. A method to describe in an approximated way the pressure radiated outside the tunnel is proposed. In the second scenario, middle and high frequency noise generated aerodynamically has been studied, including the influence of the detachment of the boundary layer around the train. A method based on a train section to quickly predict the sound pressure level inside and outside the train has been proposed. Experimental test have been performed on board to evaluate the pressure power spectra on the surface of the train, and the transmissibility of the junctions between the structure and trim. These experimental results have been used in the vibroacoustic models. The low frequency pressure waves generated with the train during the tunnel crossing has been identified in the pressure spectrum. The train characteristic section method is especially useful at high frequencies, when the whole train can be modeled by assembling different sections using the statistical energy analysis. The sound pressure level inside the train is evaluated inside and outside the tunnel.

A packing computational method relating fractal particle size distribution and void fraction in granular media

The study of granular systems is of great interest to many fields of science and technology. The packing of particles affects to the physical properties of the granular system. In particular, the crucial influence of particle size distribution (PSD) on the random packing structure increase the interest in relating both, either theoretically or by computational methods. A packing computational method is developed in order to estimate the void fraction corresponding to a fractal-like particle size distribution.

Computational study of atomic mobility for bcc phase in Ti-Al-Fe system

Experimental diffusion data were critically assessed to develop the atomic mobility for the bcc phase of the Ti–Al–Fe system by using the DICTRA software. Good agreements were obtained from comprehensive comparisons made between the calculated and the experimental diffusion coefficients. The developed atomic mobility was then validated by well predicting the interdiffusion behavior observed from the diffusion-couple experiments in available literature.

Generation of human computational models with machine learning

Services in smart environments pursue to increase the quality of people?s lives. The most important issues when developing this kind of environments is testing and validating such services. These tasks usually imply high costs and annoying or unfeasible real-world testing. In such cases, artificial societies may be used to simulate the smart environment (i.e. physical environment, equipment and humans). With this aim, the CHROMUBE methodology guides test engineers when modeling human beings. Such models reproduce behaviors which are highly similar to the real ones. Originally, these models are based on automata whose transitions are governed by random variables. Automaton?s structure and the probability distribution functions of each random variable are determined by a manual test and error process. In this paper, it is presented an alternative extension of this methodology which avoids the said manual process. It is based on learning human behavior patterns automatically from sensor data by using machine learning techniques. The presented approach has been tested on a real scenario, where this extension has given highly accurate human behavior models,

A Packing Computational Method Relating Fractal Particle Size Distribution and Void Fraction in Granular Media

The study of granular systems is of great interest to many fields of science and technology. The packing of particles affects to the physical properties of the granular system. In particular, the crucial influence of particle size distribution (PSD) on the random packing structure increase the interest in relating both, either theoretically or by computational methods. A packing computational method is developed in order to estimate the void fraction corresponding to a fractal-like particle size distribution.

Non uniform embedding based on relevance analysis with reduced computational complexity: application to the detection of pathologies from biosignal recordings

Nonlinear analysis tools for studying and characterizing the dynamics of physiological signals have gained popularity, mainly because tracking sudden alterations of the inherent complexity of biological processes might be an indicator of altered physiological states. Typically, in order to perform an analysis with such tools, the physiological variables that describe the biological process under study are used to reconstruct the underlying dynamics of the biological processes. For that goal, a procedure called time-delay or uniform embedding is usually employed. Nonetheless, there is evidence of its inability for dealing with non-stationary signals, as those recorded from many physiological processes. To handle with such a drawback, this paper evaluates the utility of non-conventional time series reconstruction procedures based on non uniform embedding, applying them to automatic pattern recognition tasks. The paper compares a state of the art non uniform approach with a novel scheme which fuses embedding and feature selection at once, searching for better reconstructions of the dynamics of the system. Moreover, results are also compared with two classic uniform embedding techniques. Thus, the goal is comparing uniform and non uniform reconstruction techniques, including the one proposed in this work, for pattern recognition in biomedical signal processing tasks. Once the state space is reconstructed, the scheme followed characterizes with three classic nonlinear dynamic features (Largest Lyapunov Exponent, Correlation Dimension and Recurrence Period Density Entropy), while classification is carried out by means of a simple k-nn classifier. In order to test its generalization capabilities, the approach was tested with three different physiological databases (Speech Pathologies, Epilepsy and Heart Murmurs). In terms of the accuracy obtained to automatically detect the presence of pathologies, and for the three types of biosignals analyzed, the non uniform techniques used in this work lightly outperformed the results obtained using the uniform methods, suggesting their usefulness to characterize non-stationary biomedical signals in pattern recognition applications. On the other hand, in view of the results obtained and its low computational load, the proposed technique suggests its applicability for the applications under study.

A computational model coupling mechanics and electrophysiology in spinal cord injury

Traumatic brain injury and spinal cord injury have recently been put under the spotlight as major causes of death and disability in the developed world. Despite the important ongoing experimental and modeling campaigns aimed at understanding the mechanics of tissue and cell damage typically observed in such events, the differentiated roles of strain, stress and their corresponding loading rates on the damage level itself remain unclear. More specifically, the direct relations between brain and spinal cord tissue or cell damage, and electrophysiological functions are still to be unraveled. Whereas mechanical modeling efforts are focusing mainly on stress distribution and mechanistic-based damage criteria, simulated function-based damage criteria are still missing. Here, we propose a new multiscale model of myelinated axon associating electrophysiological impairment to structural damage as a function of strain and strain rate. This multiscale approach provides a new framework for damage evaluation directly relating neuron mechanics and electrophysiological properties, thus providing a link between mechanical trauma and subsequent functional deficits

A computational model of the anterior intraparietal area

The monkey anterior intraparietal area (AIP) encodes visual information about three-dimensional object shape that is used to shape the hand for grasping. In robotics a similar role has been played by modules that fit point cloud data to the superquadric family of shapes and its various extensions. We developed a model of shape tuning in AIP based on cosine tuning to superquadric parameters. However, the model did not fit the data well, and we also found that it was difficult to accurately reproduce these parameters using neural networks with the appropriate inputs (modelled on the caudal intraparietal area, CIP). The latter difficulty was related to the fact that there are large discontinuities in the superquadric parameters between very similar shapes. To address these limitations we adopted an alternative shape parameterization based on an Isomap nonlinear dimension reduction. The Isomap was built using gradients and curvatures of object surface depth. This alternative parameterization was low-dimensional (like superquadrics), but data-driven (similar to an alternative clustering approach that is also sometimes used in robotics) and lacked large discontinuities. Isomaps with 16 or more dimensions reproduced the AIP data fairly well. Moreover, we found that the Isomap parameters could be approximated from CIP-like input much more accurately than the superquadric parameters. We conclude that Isomaps, or perhaps alternative dimension reductions of CIP signals, provide a promising model of AIP tuning. We have now started to integrate our model with a robot hand, to explore the efficacy of Isomap shape reductions in grasp planning. Future work will consider dynamics of spike responses and integration with related visual and motor area models.

A semantic-based approach to attain reproducibility of computational environments in scientific workflows: a case study

Reproducible research in scientific workflows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and final results, improves understanding, and permits replaying a workflow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We define a process for documenting the workflow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation using a real workflow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms.

Logarithmical hopping encoding: a low computational complexity algorithm for image compression

LHE (logarithmical hopping encoding) is a computationally efficient image compression algorithm that exploits the Weber–Fechner law to encode the error between colour component predictions and the actual value of such components. More concretely, for each pixel, luminance and chrominance predictions are calculated as a function of the surrounding pixels and then the error between the predictions and the actual values are logarithmically quantised. The main advantage of LHE is that although it is capable of achieving a low-bit rate encoding with high quality results in terms of peak signal-to-noise ratio (PSNR) and image quality metrics with full-reference (FSIM) and non-reference (blind/referenceless image spatial quality evaluator), its time complexity is O( n) and its memory complexity is O(1). Furthermore, an enhanced version of the algorithm is proposed, where the output codes provided by the logarithmical quantiser are used in a pre-processing stage to estimate the perceptual relevance of the image blocks. This allows the algorithm to downsample the blocks with low perceptual relevance, thus improving the compression rate. The performance of LHE is especially remarkable when the bit per pixel rate is low, showing much better quality, in terms of PSNR and FSIM, than JPEG and slightly lower quality than JPEG-2000 but being more computationally efficient.