DMT of Multihop Networks: End Points and Computational Tools

In this paper, the diversity-multiplexing gain tradeoff (DMT) of single-source, single-sink (ss-ss), multihop relay networks having slow-fading links is studied. In particular, the two end-points of the DMT of ss-ss full-duplex networks are determined, by showing that the maximum achievable diversity gain is equal to the min-cut and that the maximum multiplexing gain is equal to the min-cut rank, the latter by using an operational connection to a deterministic network. Also included in the paper, are several results that aid in the computation of the DMT of networks operating under amplify-and-forward (AF) protocols. In particular, it is shown that the colored noise encountered in amplify-and-forward protocols can be treated as white for the purpose of DMT computation, lower bounds on the DMT of lower-triangular channel matrices are derived and the DMT of parallel MIMO channels is computed. All protocols appearing in the paper are explicit and rely only upon AF relaying. Half-duplex networks and explicit coding schemes are studied in a companion paper.

Computational tools for mechanistic discrimination in the reductive and metathesis coupling reactions mediated by titanium(IV) isopropoxide

A theoretical study has been carried out at the B3LYP/LANL2DZ level to compare the reactivity of phenyl isocyanate and phenyl isothiocyanate towards titanium(IV) alkoxides. Isocyanates are shown to favour both mono insertion and double insertion reactions. Double insertion in a head-to-tail fashion is shown to be more exothermic than double insertion in a head-to-head fashion. The head-to-head double insertion leads to the metathesis product, a carbodiimide, after the extrusion of carbon dioxide. In the case of phenyl isothiocyanate, calculations favour the formation of only mono insertion products. Formation of a double insertion product is highly unfavourable. Further, these studies indicate that the reverse reaction involving the metathesis of N,N-'-diphenyl carbodiimide with carbon dioxide is likely to proceed more efficiently than the metathesis reaction with carbon disulphide. This is in excellent agreement with experimental results as metathesis with carbon disulphide fails to occur. In a second study, multilayer MM/QM calculations are carried out on intermediates generated from reduction of titanium(IV) alkoxides to investigate the effect of alkoxy bridging on the reactivity of multinuclear Ti species. Bimolecular coupling of imines initiated by Ti(III) species leads to a mixture of diastereomers and not diastereoselective coupling of the imine. However if the reaction is carried out by a trimeric biradical species, diastereoselective coupling of the imine is predicted. The presence of alkoxy bridges greatly favours the formation of the d,l (+/-) isomer, whereas the intermediate without alkoxy bridges favours the more stable meso isomer. As a bridged trimeric species, stabilized by bridging alkoxy groups, correctly explains the diastereoselective reaction, it is the most likely intermediate in the reaction.

Computational tools for comparing asymmetric GARCH models via Bayes factors

In this paper we use Markov chain Monte Carlo (MCMC) methods in order to estimate and compare GARCH models from a Bayesian perspective. We allow for possibly heavy tailed and asymmetric distributions in the error term. We use a general method proposed in the literature to introduce skewness into a continuous unimodal and symmetric distribution. For each model we compute an approximation to the marginal likelihood, based on the MCMC output. From these approximations we compute Bayes factors and posterior model probabilities. (C) 2012 IMACS. Published by Elsevier B.V. All rights reserved.

Development of one-dimensional and two-dimensional computational tools that simulate steady internal condensing flows in terrestrial and zero-gravity environments

This dissertation presents an effective quasi one-dimensional (1-D) computational simulation tool and a full two-dimensional (2-D) computational simulation methodology for steady annular/stratified internal condensing flows of pure vapor. These simulation tools are used to investigate internal condensing flows in both gravity as well as shear driven environments. Through accurate numerical simulations of the full two dimensional governing equations, results for laminar/laminar condensing flows inside mm-scale ducts are presented. The methodology has been developed using MATLAB/COMSOL platform and is currently capable of simulating film-wise condensation for steady (and unsteady flows). Moreover, a novel 1-D solution technique, capable of simulating condensing flows inside rectangular and circular ducts with different thermal boundary conditions is also presented. The results obtained from the 2-D scientific tool and 1-D engineering tool, are validated and synthesized with experimental results for gravity dominated flows inside vertical tube and inclined channel; and, also, for shear/pressure driven flows inside horizontal channels. Furthermore, these simulation tools are employed to demonstrate key differences of physics between gravity dominated and shear/pressure driven flows. A transition map that distinguishes shear driven, gravity driven, and “mixed” driven flow zones within the non-dimensional parameter space that govern these duct flows is presented along with the film thickness and heat transfer correlations that are valid in these zones. It has also been shown that internal condensing flows in a micro-meter scale duct experiences shear driven flow, even in different gravitational environments. The full 2-D steady computational tool has been employed to investigate the length of annularity. The result for a shear driven flow in a horizontal channel shows that in absence of any noise or pressure fluctuation at the inlet, the onset of non-annularity is partly due to insufficient shear at the liquid-vapor interface. This result is being further corroborated/investigated by R. R. Naik with the help of the unsteady simulation tool. The condensing flow results and flow physics understanding developed through these simulation tools will be instrumental in reliable design of modern micro-scale and spacebased thermal systems.

Computational tools to investigate genetic cardiac channelopathies

The aim of this perspective article is to share with the community of ion channel scientists our thoughts and expectations regarding the increasing role that computational tools will play in the future of our field. The opinions and comments detailed here are the result of a 3-day long international exploratory workshop that took place in October 2013 and that was supported by the Swiss National Science Foundation.

Computational Tools for Stereo and Light Field Photography

This thesis covers a broad part of the field of computational photography, including video stabilization and image warping techniques, introductions to light field photography and the conversion of monocular images and videos into stereoscopic 3D content. We present a user assisted technique for stereoscopic 3D conversion from 2D images. Our approach exploits the geometric structure of perspective images including vanishing points. We allow a user to indicate lines, planes, and vanishing points in the input image, and directly employ these as guides of an image warp that produces a stereo image pair. Our method is most suitable for scenes with large scale structures such as buildings and is able to skip the step of constructing a depth map. Further, we propose a method to acquire 3D light fields using a hand-held camera, and describe several computational photography applications facilitated by our approach. As the input we take an image sequence from a camera translating along an approximately linear path with limited camera rotations. Users can acquire such data easily in a few seconds by moving a hand-held camera. We convert the input into a regularly sampled 3D light field by resampling and aligning them in the spatio-temporal domain. We also present a novel technique for high-quality disparity estimation from light fields. Finally, we show applications including digital refocusing and synthetic aperture blur, foreground removal, selective colorization, and others.

Core physics and safety analysis of Generation-IV Sodium Fast Reactors using existing and newly developed computational tools

El futuro de la energía nuclear de fisión dependerá, entre otros factores, de la capacidad que las nuevas tecnologías demuestren para solventar los principales retos a largo plazo que se plantean. Los principales retos se pueden resumir en los siguientes aspectos: la capacidad de proporcionar una solución final, segura y fiable a los residuos radiactivos; así como dar solución a la limitación de recursos naturales necesarios para alimentar los reactores nucleares; y por último, una mejora robusta en la seguridad de las centrales que en definitiva evite cualquier daño potencial tanto en la población como en el medio ambiente como consecuencia de cualquier escenario imaginable o más allá de lo imaginable. Siguiendo estas motivaciones, la Generación IV de reactores nucleares surge con el compromiso de proporcionar electricidad de forma sostenible, segura, económica y evitando la proliferación de material fisible. Entre los sistemas conceptuales que se consideran para la Gen IV, los reactores rápidos destacan por su capacidad potencial de transmutar actínidos a la vez que permiten una utilización óptima de los recursos naturales. Entre los refrigerantes que se plantean, el sodio parece una de las soluciones más prometedoras. Como consecuencia, esta tesis surgió dentro del marco del proyecto europeo CP-ESFR con el principal objetivo de evaluar la física de núcleo y seguridad de los reactores rápidos refrigerados por sodio, al tiempo que se desarrollaron herramientas apropiadas para dichos análisis. Efectivamente, en una primera parte de la tesis, se abarca el estudio de la física del núcleo de un reactor rápido representativo, incluyendo el análisis detallado de la capacidad de transmutar actínidos minoritarios. Como resultado de dichos análisis, se publicó un artículo en la revista Annals of Nuclear Energy [96]. Por otra parte, a través de un análisis de un hipotético escenario nuclear español, se evalúo la disponibilidad de recursos naturales necesarios en el caso particular de España para alimentar una flota específica de reactores rápidos, siguiendo varios escenarios de demanda, y teniendo en cuenta la capacidad de reproducción de plutonio que tienen estos sistemas. Como resultado de este trabajo también surgió una publicación en otra revista científica de prestigio internacional como es Energy Conversion and Management [97]. Con objeto de realizar esos y otros análisis, se desarrollaron diversos modelos del núcleo del ESFR siguiendo varias configuraciones, y para diferentes códigos. Por otro lado, con objeto de poder realizar análisis de seguridad de reactores rápidos, son necesarias herramientas multidimensionales de alta fidelidad específicas para reactores rápidos. Dichas herramientas deben integrar fenómenos relacionados con la neutrónica y con la termo-hidráulica, entre otros, mediante una aproximación multi-física. Siguiendo este objetivo, se evalúo el código de difusión neutrónica ANDES para su aplicación a reactores rápidos. ANDES es un código de resolución nodal que se encuentra implementado dentro del sistema COBAYA3 y está basado en el método ACMFD. Por lo tanto, el método ACMFD fue sometido a una revisión en profundidad para evaluar su aptitud para la aplicación a reactores rápidos. Durante ese proceso, se identificaron determinadas limitaciones que se discutirán a lo largo de este trabajo, junto con los desarrollos que se han elaborado e implementado para la resolución de dichas dificultades. Por otra parte, se desarrolló satisfactoriamente el acomplamiento del código neutrónico ANDES con un código termo-hidráulico de subcanales llamado SUBCHANFLOW, desarrollado recientemente en el KIT. Como conclusión de esta parte, todos los desarrollos implementados son evaluados y verificados. En paralelo con esos desarrollos, se calcularon para el núcleo del ESFR las secciones eficaces en multigrupos homogeneizadas a nivel nodal, así como otros parámetros neutrónicos, mediante los códigos ERANOS, primero, y SERPENT, después. Dichos parámetros se utilizaron más adelante para realizar cálculos estacionarios con ANDES. Además, como consecuencia de la contribución de la UPM al paquete de seguridad del proyecto CP-ESFR, se calcularon mediante el código SERPENT los parámetros de cinética puntual que se necesitan introducir en los típicos códigos termo-hidráulicos de planta, para estudios de seguridad. En concreto, dichos parámetros sirvieron para el análisis del impacto que tienen los actínidos minoritarios en el comportamiento de transitorios. Concluyendo, la tesis presenta una aproximación sistemática y multidisciplinar aplicada al análisis de seguridad y comportamiento neutrónico de los reactores rápidos de sodio de la Gen-IV, usando herramientas de cálculo existentes y recién desarrolladas ad' hoc para tal aplicación. Se ha empleado una cantidad importante de tiempo en identificar limitaciones de los métodos nodales analíticos en su aplicación en multigrupos a reactores rápidos, y se proponen interesantes soluciones para abordarlas. ABSTRACT The future of nuclear reactors will depend, among other aspects, on the capability to solve the long-term challenges linked to this technology. These are the capability to provide a definite, safe and reliable solution to the nuclear wastes; the limitation of natural resources, needed to fuel the reactors; and last but not least, the improved safety, which would avoid any potential damage on the public and or environment as a consequence of any imaginable and beyond imaginable circumstance. Following these motivations, the IV Generation of nuclear reactors arises, with the aim to provide sustainable, safe, economic and proliferationresistant electricity. Among the systems considered for the Gen IV, fast reactors have a representative role thanks to their potential capacity to transmute actinides together with the optimal usage of natural resources, being the sodium fast reactors the most promising concept. As a consequence, this thesis was born in the framework of the CP-ESFR project with the generic aim of evaluating the core physics and safety of sodium fast reactors, as well as the development of the approppriated tools to perform such analyses. Indeed, in a first part of this thesis work, the main core physics of the representative sodium fast reactor are assessed, including a detailed analysis of the capability to transmute minor actinides. A part of the results obtained have been published in Annals of Nuclear Energy [96]. Moreover, by means of the analysis of a hypothetical Spanish nuclear scenario, the availability of natural resources required to deploy an specific fleet of fast reactor is assessed, taking into account the breeding properties of such systems. This work also led to a publication in Energy Conversion and Management [97]. In order to perform those and other analyses, several models of the ESFR core were created for different codes. On the other hand, in order to perform safety studies of sodium fast reactors, high fidelity multidimensional analysis tools for sodium fast reactors are required. Such tools should integrate neutronic and thermal-hydraulic phenomena in a multi-physics approach. Following this motivation, the neutron diffusion code ANDES is assessed for sodium fast reactor applications. ANDES is the nodal solver implemented inside the multigroup pin-by-pin diffusion COBAYA3 code, and is based on the analytical method ACMFD. Thus, the ACMFD was verified for SFR applications and while doing so, some limitations were encountered, which are discussed through this work. In order to solve those, some new developments are proposed and implemented in ANDES. Moreover, the code was satisfactorily coupled with the thermal-hydraulic code SUBCHANFLOW, recently developed at KIT. Finally, the different implementations are verified. In addition to those developments, the node homogenized multigroup cross sections and other neutron parameters were obtained for the ESFR core using ERANOS and SERPENT codes, and employed afterwards by ANDES to perform steady state calculations. Moreover, as a result of the UPM contribution to the safety package of the CP-ESFR project, the point kinetic parameters required by the typical plant thermal-hydraulic codes were computed for the ESFR core using SERPENT, which final aim was the assessment of the impact of minor actinides in transient behaviour. All in all, the thesis provides a systematic and multi-purpose approach applied to the assessment of safety and performance parameters of Generation-IV SFR, using existing and newly developed analytical tools. An important amount of time was employed in identifying the limitations that the analytical nodal diffusion methods present when applied to fast reactors following a multigroup approach, and interesting solutions are proposed in order to overcome them.

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.

Assessing computational tools for the discovery of transcription factor binding sites

The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

Simulation and graph mining tools for improving gene mapping efficiency

Gene mapping is a systematic search for genes that affect observable characteristics of an organism. In this thesis we offer computational tools to improve the efficiency of (disease) gene-mapping efforts. In the first part of the thesis we propose an efficient simulation procedure for generating realistic genetical data from isolated populations. Simulated data is useful for evaluating hypothesised gene-mapping study designs and computational analysis tools. As an example of such evaluation, we demonstrate how a population-based study design can be a powerful alternative to traditional family-based designs in association-based gene-mapping projects. In the second part of the thesis we consider a prioritisation of a (typically large) set of putative disease-associated genes acquired from an initial gene-mapping analysis. Prioritisation is necessary to be able to focus on the most promising candidates. We show how to harness the current biomedical knowledge for the prioritisation task by integrating various publicly available biological databases into a weighted biological graph. We then demonstrate how to find and evaluate connections between entities, such as genes and diseases, from this unified schema by graph mining techniques. Finally, in the last part of the thesis, we define the concept of reliable subgraph and the corresponding subgraph extraction problem. Reliable subgraphs concisely describe strong and independent connections between two given vertices in a random graph, and hence they are especially useful for visualising such connections. We propose novel algorithms for extracting reliable subgraphs from large random graphs. The efficiency and scalability of the proposed graph mining methods are backed by extensive experiments on real data. While our application focus is in genetics, the concepts and algorithms can be applied to other domains as well. We demonstrate this generality by considering coauthor graphs in addition to biological graphs in the experiments.

Computational design of self-assembling proteins and protein-DNA nanowires

Computational protein design (CPD) is a burgeoning field that uses a physical-chemical or knowledge-based scoring function to create protein variants with new or improved properties. This exciting approach has recently been used to generate proteins with entirely new functions, ones that are not observed in naturally occurring proteins. For example, several enzymes were designed to catalyze reactions that are not in the repertoire of any known natural enzyme. In these designs, novel catalytic activity was built de novo (from scratch) into a previously inert protein scaffold. In addition to de novo enzyme design, the computational design of protein-protein interactions can also be used to create novel functionality, such as neutralization of influenza. Our goal here was to design a protein that can self-assemble with DNA into nanowires. We used computational tools to homodimerize a transcription factor that binds a specific sequence of double-stranded DNA. We arranged the protein-protein and protein-DNA binding sites so that the self-assembly could occur in a linear fashion to generate nanowires. Upon mixing our designed protein homodimer with the double-stranded DNA, the molecules immediately self-assembled into nanowires. This nanowire topology was confirmed using atomic force microscopy. Co-crystal structure showed that the nanowire is assembled via the desired interactions. To the best of our knowledge, this is the first example of a protein-DNA self-assembly that does not rely on covalent interactions. We anticipate that this new material will stimulate further interest in the development of advanced biomaterials.

Parallel coordinates in computational engineering design

Modern Engineering Design involves the deployment of many computational tools. Re- search on challenging real-world design problems is focused on developing improvements for the engineering design process through the integration and application of advanced com- putational search/optimization and analysis tools. Successful application of these methods generates vast quantities of data on potential optimum designs. To gain maximum value from the optimization process, designers need to visualise and interpret this information leading to better understanding of the complex and multimodal relations between param- eters, objectives and decision-making of multiple and strongly conflicting criteria. Initial work by the authors has identified that the Parallel Coordinates interactive visualisation method has considerable potential in this regard. This methodology involves significant levels of user-interaction, making the engineering designer central to the process, rather than the passive recipient of a deluge of pre-formatted information. In the present work we have applied and demonstrated this methodology in two differ- ent aerodynamic turbomachinery design cases; a detailed 3D shape design for compressor blades, and a preliminary mean-line design for the whole compressor core. The first case comprises 26 design parameters for the parameterisation of the blade geometry, and we analysed the data produced from a three-objective optimization study, thus describing a design space with 29 dimensions. The latter case comprises 45 design parameters and two objective functions, hence developing a design space with 47 dimensions. In both cases the dimensionality can be managed quite easily in Parallel Coordinates space, and most importantly, we are able to identify interesting and crucial aspects of the relationships between the design parameters and optimum level of the objective functions under con- sideration. These findings guide the human designer to find answers to questions that could not even be addressed before. In this way, understanding the design leads to more intelligent decision-making and design space exploration. © 2012 AIAA.

Web tools for the prioritization of candidate disease genes

Despite increasing sequencing capacity, genetic disease investigation still frequently results in the identification of loci containing multiple candidate disease genes that need to be tested for involvement in the disease. This process can be expedited by prioritizing the candidates prior to testing. Over the last decade, a large number of computational methods and tools have been developed to assist the clinical geneticist in prioritizing candidate disease genes. In this chapter, we give an overview of computational tools that can be used for this purpose, all of which are freely available over the web.