Computation2015, 3(3), 386-426; doi:10.3390/computation3030386 (registering DOI) - published 28 August 2015 Show/Hide Abstract
Abstract: A computational analysis is performed on the diffraction of water waves induced by large-diameter, surface-piercing, vertical circular cylinder. With reference to linear-wave cases, the phenomenon is preliminarly considered in terms of velocity potential, a simplified theoretical framework in which both hypotheses of inviscid fluid and irrotational flow are incorporated. Then, and as a first-approximation analysis, the Euler equations in primitive variables are considered (a framework in which the fluid is still handled as inviscid, but the field can be rotational). Finally, the real-fluid behavior is analyzed, by numerically integrating the full Navier-Stokes equations (viscous fluid and rotational field) in their velocity-pressure formulation, by following the approach of the Direct Numerical Simulation (DNS, no models are used for the fluctuating portion of the velocity field). For further investigation of the flow fields, the swirling-strength criterion for flow-structure extraction, and the Karhunen-Loève (KL) decomposition technique for the extraction of the most energetic flow modes respectively, are applied to the computed fields. It is found that remarkable differences exist between the wave-induced fields, as derived within the different computing frameworks tested.
Abstract: This contribution is dedicated to demonstrating the high potential and manifold applications of state-of-the-art computational fluid dynamics (CFD) tools for free-surface flows in civil and environmental engineering. All simulations were performed with the academic research code ELBE (efficient lattice boltzmann environment, http://www.tuhh.de/elbe). The ELBE code follows the supercomputing-on-the-desktop paradigm and is especially designed for local supercomputing, without tedious accesses to supercomputers. ELBE uses graphics processing units (GPU) to accelerate the computations and can be used in a single GPU-equipped workstation of, e.g., a design engineer. The code has been successfully validated in very different fields, mostly related to naval architecture and mechanical engineering. In this contribution, we give an overview of past and present applications with practical relevance for civil engineers. The presented applications are grouped into three major categories: (i) tsunami simulations, considering wave propagation, wave runup, inundation and debris flows; (ii) dam break simulations; and (iii) numerical wave tanks for the calculation of hydrodynamic loads on fixed and moving bodies. This broad range of applications in combination with accurate numerical results and very competitive times to solution demonstrates that modern CFD tools in general, and the ELBE code in particular, can be a helpful design tool for civil and environmental engineers.
Abstract: We used a previously developed simulation model of a plant cell wall and its enzymatic degradation to compare the abilities of two hemicelluloses, glucuronoarabinoxylan (GAX) and xyloglucan (XG), to protect cellulose microfibrils (CMFs) from attack by cellulose-degrading enzymes. Additionally, we investigated the effect of XG abundance on the degradation rate of CMFs in the presence of the same enzymes. Simulations were run using hypothetical cell-wall compositions in which the numbers and arrangement of CMFs and (1,3;1,4)-β-glucan were kept constant, but the proportions of GAX and XG were altered. Scenarios considered walls with low and equal proportions of either GAX or XG, and also low, medium and high proportions of XG in the absence of GAX. The rate of CMF degradation was much lower in walls with GAX than walls with XG, except for early in the simulation when the reverse held, suggesting that XGs were protecting CMFs by competitive inhibition. Increasing XG content reduced both the degradation rate of CMFs and the percent of XG degraded, indicating that activity of enzymes decreased with XG density despite XG being degradable. Glucose oligosaccharide breakdown products were analysed on the basis of the originating polysaccharide and their degree of polymerisation (DP). The presence of GAX as opposed to equal amounts of XG had some significant effects on the amount and profile of breakdown products from XG and CMFs.
Abstract: Computation of the non-central chi square probability density function is encountered in diverse fields of applied statistics and engineering. The distribution is commonly computed as a Poisson mixture of central chi square densities, where the terms of the sum are computed starting with the integer nearest the non-centrality parameter. However, for computation of the values in either tail region these terms are not the most significant and starting with them results in an increased computational load without a corresponding increase in accuracy. The most significant terms are shown to be a function of both the non-centrality parameter, the degree of freedom and the point of evaluation. A computationally simple approximate solution to the location of the most significant terms as well as the exact solution based on a Newton–Raphson iteration is presented. A quadratic approximation of the interval of summation is also developed in order to meet a requisite number of significant digits of accuracy. Computationally efficient recursions are used over these improved intervals. The method provides a means of computing the non-central chi square probability density function to a requisite accuracy as a Poisson mixture over all domains of interest.
Abstract: The European program HORIZON2020 aims to have 20% of electricity produced by renewable sources. The building sector represents 40% of the European Union energy consumption. Reducing energy consumption in buildings is therefore a priority for energy efficiency. The present investigation explores the most adequate roof shapes compatible with the placement of different types of small wind energy generators on high-rise buildings for urban wind energy exploitation. The wind flow around traditional state-of-the-art roof shapes is considered. In addition, the influence of the roof edge on the wind flow on high-rise buildings is analyzed. These geometries are investigated, both qualitatively and quantitatively, and the turbulence intensity threshold for horizontal axis wind turbines is considered. The most adequate shapes for wind energy exploitation are identified, studying vertical profiles of velocity, turbulent kinetic energy and turbulence intensity. Curved shapes are the most interesting building roof shapes from the wind energy exploitation point of view, leading to the highest speed-up and the lowest turbulence intensity.
Abstract: One fundamental problem of bioinformatics is the computational recognition of DNA and RNA binding sites. Given a set of short DNA or RNA sequences of equal length such as transcription factor binding sites or RNA splice sites, the task is to learn a pattern from this set that allows the recognition of similar sites in another set of DNA or RNA sequences. Permuted Markov (PM) models and permuted variable length Markov (PVLM) models are two powerful models for this task, but the problem of finding an optimal PM model or PVLM model is NP-hard. While the problem of finding an optimal PM model or PVLM model of order one is equivalent to the traveling salesman problem (TSP), the problem of finding an optimal PM model or PVLM model of order two is equivalent to the quadratic TSP (QTSP). Several exact algorithms exist for solving the QTSP, but it is unclear if these algorithms are capable of solving QTSP instances resulting from RNA splice sites of at least 150 base pairs in a reasonable time frame. Here, we investigate the performance of three exact algorithms for solving the QTSP for ten datasets of splice acceptor sites and splice donor sites of five different species and find that one of these algorithms is capable of solving QTSP instances of up to 200 base pairs with a running time of less than two days.