Next Issue
Volume 3, September
Previous Issue
Volume 3, March

Table of Contents

Computation, Volume 3, Issue 2 (June 2015) – 12 articles , Pages 114-335

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
Order results
Result details
Select all
Export citation of selected articles as:
Open AccessArticle
Fast Computation of the Non-Central Chi Square PDF Outside the HDR Under a Requisite Precision Constraint
Computation 2015, 3(2), 326-335; https://doi.org/10.3390/computation3020326 - 19 Jun 2015
Viewed by 2110
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 [...] Read more.
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. Full article
(This article belongs to the Section Computational Engineering)
Open AccessArticle
On Roof Geometry for Urban Wind Energy Exploitation in High-Rise Buildings
Computation 2015, 3(2), 299-325; https://doi.org/10.3390/computation3020299 - 10 Jun 2015
Cited by 10 | Viewed by 3798
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Computational Fluid Dynamics in Civil Engineering)
Show Figures

Graphical abstract

Open AccessArticle
Computational Recognition of RNA Splice Sites by Exact Algorithms for the Quadratic Traveling Salesman Problem
Computation 2015, 3(2), 285-298; https://doi.org/10.3390/computation3020285 - 03 Jun 2015
Cited by 3 | Viewed by 2850
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
Open AccessArticle
Effects of a Sprinkler on Evacuation Dynamics in Fire
Computation 2015, 3(2), 274-284; https://doi.org/10.3390/computation3020274 - 03 Jun 2015
Cited by 1 | Viewed by 2461
Abstract
A fire in an enclosed space, such as a room in a building, is generally called a compartment fire. To prevent the compartment fire, a sprinkler for first-aid fire-fighting is installed in rooms. However, it is difficult to determine the degree to which [...] Read more.
A fire in an enclosed space, such as a room in a building, is generally called a compartment fire. To prevent the compartment fire, a sprinkler for first-aid fire-fighting is installed in rooms. However, it is difficult to determine the degree to which smoke generation and the fire spreading will be inhibited when sprinklers are on. In particular, demonstrating evacuation behavior assuming an actual fire is impossible. In this study, we evaluated an effectiveness of the sprinkler by numerical simulations. To consider evacuation dynamics, a real-coded cellular automata (RCA) was used, where we can freely set the direction and velocity of an evacuee based on a floor field model. To consider the situation in the room fire, we used a simulator called Fire Dynamics Simulator (FDS). Two cases with and without the sprinkler were compared to see the validity of the sprinkler on evacuation dynamics. The effect of smoke and the expansion of the fire-spreading region were discussed. Results show that, since the fire-spreading region disappears when the sprinkler is actuated, the evacuation time decreases. Even though the sprinkler is actuated, the smoke generated at the beginning of a fire diffuses inside the whole room. However, the duration of evacuees being overwhelmed by smoke is less, because the amount of smoke generated by the pyrolysis reaction is much decreased. Full article
(This article belongs to the Special Issue Computational Fluid Dynamics in Civil Engineering)
Show Figures

Figure 1

Open AccessArticle
LES: Unsteady Atmospheric Turbulent Layer Inlet. A Precursor Method Application and Its Quality Check
Computation 2015, 3(2), 262-273; https://doi.org/10.3390/computation3020262 - 26 May 2015
Viewed by 2045
Abstract
The motivation of this work is to bridge the gap between experimental approaches in wind tunnel testing and numerical computations, in the field of structural design against strong winds. This paper focuses on the generation of an unsteady flow field, representative of a [...] Read more.
The motivation of this work is to bridge the gap between experimental approaches in wind tunnel testing and numerical computations, in the field of structural design against strong winds. This paper focuses on the generation of an unsteady flow field, representative of a natural wind field, but still compatible with Computational Fluid Dynamics inlet requirements. A simple and “naive” procedure is explained, and the results are in good agreement with some international standards. Full article
(This article belongs to the Special Issue Computational Fluid Dynamics in Civil Engineering)
Show Figures

Figure 1

Open AccessArticle
Engineering-Based Thermal CFD Simulations on Massive Parallel Systems
Computation 2015, 3(2), 235-261; https://doi.org/10.3390/computation3020235 - 22 May 2015
Cited by 3 | Viewed by 2747
Abstract
The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this [...] Read more.
The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this paper, we present a hierarchical data structure for massive parallel computations that supports the coupling of a Navier–Stokes-based fluid flow code with the Boussinesq approximation in order to address complex thermal scenarios for energy-related assessments. The newly designed data structure is specifically designed with the idea of interactive data exploration and visualization during runtime of the simulation code; a major shortcoming of traditional high-performance computing (HPC) simulation codes. We further show and discuss speed-up values obtained on one of Germany’s top-ranked supercomputers with up to 140,000 processes and present simulation results for different engineering-based thermal problems. Full article
(This article belongs to the Special Issue Computational Fluid Dynamics in Civil Engineering)
Open AccessCommunication
Computational Approach to 3D Modeling of the Lymph Node Geometry
Computation 2015, 3(2), 222-234; https://doi.org/10.3390/computation3020222 - 22 May 2015
Cited by 19 | Viewed by 4359
Abstract
In this study we present a computational approach to the generation of the major geometric structures of an idealized murine lymph node (LN). In this generation, we consider the major compartments such as the subcapsular sinus, B cell follicles, trabecular and medullar sinuses, [...] Read more.
In this study we present a computational approach to the generation of the major geometric structures of an idealized murine lymph node (LN). In this generation, we consider the major compartments such as the subcapsular sinus, B cell follicles, trabecular and medullar sinuses, blood vessels and the T cell zone with a primary focus on the fibroblastic reticular cell (FRC) network. Confocal microscopy data of LN macroscopic structures and structural properties of the FRC network have been generated and utilized in the present model. The methodology sets a library of modules that can be used to assemble a solid geometric LN model and subsequently generate an adaptive mesh model capable of implementing transport phenomena. Overall, based on the use of high-resolution confocal microscopy and morphological analysis of cell 3D reconstructions, we have developed a computational model of the LN geometry, suitable for further investigation in studies of fluid transport and cell migration in this immunologically essential organ. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)
Show Figures

Graphical abstract

Open AccessReview
Simulation Frameworks for Morphogenetic Problems
Computation 2015, 3(2), 197-221; https://doi.org/10.3390/computation3020197 - 24 Apr 2015
Cited by 18 | Viewed by 3422
Abstract
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has been [...] Read more.
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has been discussed and used in a multitude of works, the realistic modelling of the tissue has only started on a larger scale in the last decade. Here, common tissue modelling techniques are reviewed. Besides the continuum approach, the principles and main applications of the spheroid, vertex, Cellular Potts, Immersed Boundary and Subcellular Element models are discussed in detail. In recent years, many software frameworks, implementing the aforementioned methods, have been developed. The most widely used frameworks and modelling markup languages and standards are presented. Full article
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)
Open AccessArticle
A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
Computation 2015, 3(2), 177-196; https://doi.org/10.3390/computation3020177 - 15 Apr 2015
Cited by 9 | Viewed by 9498
Abstract
There are numerous phylogenetic reconstruction methods and models available—but which should you use and why? Important considerations in phylogenetic analyses include data quality, structure, signal, alignment length and sampling. If poorly modelled, variation in rates of change across proteins and across lineages can [...] Read more.
There are numerous phylogenetic reconstruction methods and models available—but which should you use and why? Important considerations in phylogenetic analyses include data quality, structure, signal, alignment length and sampling. If poorly modelled, variation in rates of change across proteins and across lineages can lead to incorrect phylogeny reconstruction which can then lead to downstream misinterpretation of the underlying data. The risk of choosing and applying an inappropriate model can be reduced with some critical yet straightforward steps outlined in this paper. We use the question of the position of the root of placental mammals as our working example to illustrate the topological impact of model misspecification. Using this case study we focus on using models in a Bayesian framework and we outline the steps involved in identifying and assessing better fitting models for specific datasets. Full article
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
Show Figures

Figure 1

Open AccessArticle
Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response
Computation 2015, 3(2), 150-176; https://doi.org/10.3390/computation3020150 - 08 Apr 2015
Cited by 6 | Viewed by 3480
Abstract
Computational and mathematical modeling is important in support of a better understanding of complex behavior in biology. For the investigation of biological systems, researchers have used computers to construct, verify, and validate models that describe the mechanisms behind biological processes in multi-scale representations. [...] Read more.
Computational and mathematical modeling is important in support of a better understanding of complex behavior in biology. For the investigation of biological systems, researchers have used computers to construct, verify, and validate models that describe the mechanisms behind biological processes in multi-scale representations. In this paper we combine Petri net models that represent the mycobacterial infection process and innate immune response at various levels of organization, from molecular interaction to granuloma dissemination. In addition to the conventional graphical representation of the Petri net, the outcome of the model is projected onto a 3D model representing the zebrafish embryo. In this manner we provide a visualization of the process in a simulation framework that portrays the infection in the living system. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)
Show Figures

Figure 1

Open AccessArticle
CFD Simulation and Optimisation of a Low Energy Ventilation and Cooling System
Computation 2015, 3(2), 128-149; https://doi.org/10.3390/computation3020128 - 02 Apr 2015
Cited by 23 | Viewed by 5902
Abstract
Mechanical Heating Ventilation and Air-Conditioning (HVAC) systems account for 60% of the total energy consumption of buildings. As a sector, buildings contributes about 40% of the total global energy demand. By using passive technology coupled with natural ventilation from wind towers, significant amounts [...] Read more.
Mechanical Heating Ventilation and Air-Conditioning (HVAC) systems account for 60% of the total energy consumption of buildings. As a sector, buildings contributes about 40% of the total global energy demand. By using passive technology coupled with natural ventilation from wind towers, significant amounts of energy can be saved, reducing the emissions of greenhouse gases. In this study, the development of Computational Fluid Dynamics (CFD) analysis in aiding the development of wind towers was explored. Initial concepts of simple wind tower mechanics to detailed design of wind towers which integrate modifications specifically to improve the efficiency of wind towers were detailed. From this, using CFD analysis, heat transfer devices were integrated into a wind tower to provide cooling for incoming air, thus negating the reliance on mechanical HVAC systems. A commercial CFD code Fluent was used in this study to simulate the airflow inside the wind tower model with the heat transfer devices. Scaled wind tunnel testing was used to validate the computational model. The airflow supply velocity was measured and compared with the numerical results and good correlation was observed. Additionally, the spacing between the heat transfer devices was varied to optimise the performance. The technology presented here is subject to a patent application (PCT/GB2014/052263). Full article
(This article belongs to the Special Issue Computational Fluid Dynamics in Civil Engineering)
Show Figures

Graphical abstract

Open AccessArticle
Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes
Computation 2015, 3(2), 114-127; https://doi.org/10.3390/computation3020114 - 26 Mar 2015
Cited by 3 | Viewed by 3037
Abstract
Phylogenetic (tree-based) approaches to understanding evolutionary history are unable to incorporate convergent evolutionary events where two genes merge into one. In this study, as exemplars of what can be achieved when a tree is not assumed a priori, we have analysed the evolutionary [...] Read more.
Phylogenetic (tree-based) approaches to understanding evolutionary history are unable to incorporate convergent evolutionary events where two genes merge into one. In this study, as exemplars of what can be achieved when a tree is not assumed a priori, we have analysed the evolutionary histories of polyketide synthase genes and antibiotic resistance genes and have shown that their history is replete with convergent events as well as divergent events. We demonstrate that the overall histories of these genes more closely resembles the remodelling that might be seen with the children’s toy Lego, than the standard model of the phylogenetic tree. This work demonstrates further that genes can act as public goods, available for re-use and incorporation into other genetic goods. Full article
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
Show Figures

Figure 1

Previous Issue
Next Issue
Back to TopTop