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  Subjects -> ENGINEERING (Total: 2270 journals)
    - CHEMICAL ENGINEERING (191 journals)
    - CIVIL ENGINEERING (183 journals)
    - ELECTRICAL ENGINEERING (99 journals)
    - ENGINEERING (1199 journals)
    - ENGINEERING MECHANICS AND MATERIALS (390 journals)
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ENGINEERING (1199 journals)                  1 2 3 4 5 6 | Last

Showing 1 - 200 of 1205 Journals sorted alphabetically
3 Biotech     Open Access   (Followers: 7)
3D Research     Hybrid Journal   (Followers: 19)
AAPG Bulletin     Full-text available via subscription   (Followers: 5)
AASRI Procedia     Open Access   (Followers: 15)
Abstract and Applied Analysis     Open Access   (Followers: 3)
Aceh International Journal of Science and Technology     Open Access   (Followers: 2)
ACS Nano     Full-text available via subscription   (Followers: 217)
Acta Geotechnica     Hybrid Journal   (Followers: 6)
Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 5)
Acta Polytechnica : Journal of Advanced Engineering     Open Access   (Followers: 2)
Acta Scientiarum. Technology     Open Access   (Followers: 3)
Acta Universitatis Cibiniensis. Technical Series     Open Access  
Active and Passive Electronic Components     Open Access   (Followers: 7)
Adaptive Behavior     Hybrid Journal   (Followers: 10)
Adıyaman Üniversitesi Mühendislik Bilimleri Dergisi     Open Access  
Adsorption     Hybrid Journal   (Followers: 4)
Advanced Engineering Forum     Full-text available via subscription   (Followers: 4)
Advanced Science     Open Access   (Followers: 4)
Advanced Science Focus     Free   (Followers: 3)
Advanced Science Letters     Full-text available via subscription   (Followers: 5)
Advanced Science, Engineering and Medicine     Partially Free   (Followers: 7)
Advanced Synthesis & Catalysis     Hybrid Journal   (Followers: 17)
Advances in Artificial Neural Systems     Open Access   (Followers: 4)
Advances in Calculus of Variations     Hybrid Journal   (Followers: 2)
Advances in Catalysis     Full-text available via subscription   (Followers: 5)
Advances in Complex Systems     Hybrid Journal   (Followers: 7)
Advances in Engineering Software     Hybrid Journal   (Followers: 25)
Advances in Fuel Cells     Full-text available via subscription   (Followers: 14)
Advances in Fuzzy Systems     Open Access   (Followers: 5)
Advances in Geosciences (ADGEO)     Open Access   (Followers: 9)
Advances in Heat Transfer     Full-text available via subscription   (Followers: 19)
Advances in Human Factors/Ergonomics     Full-text available via subscription   (Followers: 23)
Advances in Magnetic and Optical Resonance     Full-text available via subscription   (Followers: 8)
Advances in Natural Sciences: Nanoscience and Nanotechnology     Open Access   (Followers: 28)
Advances in Operations Research     Open Access   (Followers: 11)
Advances in OptoElectronics     Open Access   (Followers: 5)
Advances in Physics Theories and Applications     Open Access   (Followers: 12)
Advances in Polymer Science     Hybrid Journal   (Followers: 40)
Advances in Porous Media     Full-text available via subscription   (Followers: 4)
Advances in Remote Sensing     Open Access   (Followers: 35)
Advances in Science and Research (ASR)     Open Access   (Followers: 6)
Aerobiologia     Hybrid Journal   (Followers: 1)
African Journal of Science, Technology, Innovation and Development     Hybrid Journal   (Followers: 4)
AIChE Journal     Hybrid Journal   (Followers: 28)
Ain Shams Engineering Journal     Open Access   (Followers: 5)
Akademik Platform Mühendislik ve Fen Bilimleri Dergisi     Open Access  
Alexandria Engineering Journal     Open Access   (Followers: 1)
AMB Express     Open Access   (Followers: 1)
American Journal of Applied Sciences     Open Access   (Followers: 27)
American Journal of Engineering and Applied Sciences     Open Access   (Followers: 11)
American Journal of Engineering Education     Open Access   (Followers: 9)
American Journal of Environmental Engineering     Open Access   (Followers: 16)
American Journal of Industrial and Business Management     Open Access   (Followers: 23)
Analele Universitatii Ovidius Constanta - Seria Chimie     Open Access  
Annals of Combinatorics     Hybrid Journal   (Followers: 3)
Annals of Pure and Applied Logic     Open Access   (Followers: 2)
Annals of Regional Science     Hybrid Journal   (Followers: 7)
Annals of Science     Hybrid Journal   (Followers: 7)
Applicable Algebra in Engineering, Communication and Computing     Hybrid Journal   (Followers: 2)
Applicable Analysis: An International Journal     Hybrid Journal   (Followers: 1)
Applied Catalysis A: General     Hybrid Journal   (Followers: 6)
Applied Catalysis B: Environmental     Hybrid Journal   (Followers: 8)
Applied Clay Science     Hybrid Journal   (Followers: 4)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 12)
Applied Magnetic Resonance     Hybrid Journal   (Followers: 3)
Applied Nanoscience     Open Access   (Followers: 7)
Applied Network Science     Open Access  
Applied Numerical Mathematics     Hybrid Journal   (Followers: 5)
Applied Physics Research     Open Access   (Followers: 3)
Applied Sciences     Open Access   (Followers: 2)
Applied Spatial Analysis and Policy     Hybrid Journal   (Followers: 4)
Arabian Journal for Science and Engineering     Hybrid Journal   (Followers: 5)
Archives of Computational Methods in Engineering     Hybrid Journal   (Followers: 4)
Archives of Foundry Engineering     Open Access  
Archives of Thermodynamics     Open Access   (Followers: 7)
Arkiv för Matematik     Hybrid Journal   (Followers: 1)
ASEE Prism     Full-text available via subscription   (Followers: 2)
Asian Engineering Review     Open Access  
Asian Journal of Applied Science and Engineering     Open Access   (Followers: 1)
Asian Journal of Applied Sciences     Open Access   (Followers: 2)
Asian Journal of Biotechnology     Open Access   (Followers: 7)
Asian Journal of Control     Hybrid Journal  
Asian Journal of Current Engineering & Maths     Open Access  
Asian Journal of Technology Innovation     Hybrid Journal   (Followers: 8)
Assembly Automation     Hybrid Journal   (Followers: 2)
at - Automatisierungstechnik     Hybrid Journal   (Followers: 1)
ATZagenda     Hybrid Journal  
ATZextra worldwide     Hybrid Journal  
Australasian Physical & Engineering Sciences in Medicine     Hybrid Journal   (Followers: 1)
Australian Journal of Multi-Disciplinary Engineering     Full-text available via subscription   (Followers: 2)
Autonomous Mental Development, IEEE Transactions on     Hybrid Journal   (Followers: 7)
Avances en Ciencias e Ingeniería     Open Access  
Balkan Region Conference on Engineering and Business Education     Open Access   (Followers: 1)
Bangladesh Journal of Scientific and Industrial Research     Open Access  
Basin Research     Hybrid Journal   (Followers: 3)
Batteries     Open Access   (Followers: 3)
Bautechnik     Hybrid Journal   (Followers: 1)
Bell Labs Technical Journal     Hybrid Journal   (Followers: 23)
Beni-Suef University Journal of Basic and Applied Sciences     Open Access   (Followers: 3)
BER : Manufacturing Survey : Full Survey     Full-text available via subscription   (Followers: 2)
BER : Motor Trade Survey     Full-text available via subscription   (Followers: 1)
BER : Retail Sector Survey     Full-text available via subscription   (Followers: 2)
BER : Retail Survey : Full Survey     Full-text available via subscription   (Followers: 2)
BER : Survey of Business Conditions in Manufacturing : An Executive Summary     Full-text available via subscription   (Followers: 3)
BER : Survey of Business Conditions in Retail : An Executive Summary     Full-text available via subscription   (Followers: 3)
Bharatiya Vaigyanik evam Audyogik Anusandhan Patrika (BVAAP)     Open Access   (Followers: 1)
Biofuels Engineering     Open Access  
Biointerphases     Open Access   (Followers: 1)
Biomaterials Science     Full-text available via subscription   (Followers: 9)
Biomedical Engineering     Hybrid Journal   (Followers: 16)
Biomedical Engineering and Computational Biology     Open Access   (Followers: 13)
Biomedical Engineering Letters     Hybrid Journal   (Followers: 5)
Biomedical Engineering, IEEE Reviews in     Full-text available via subscription   (Followers: 16)
Biomedical Engineering, IEEE Transactions on     Hybrid Journal   (Followers: 31)
Biomedical Engineering: Applications, Basis and Communications     Hybrid Journal   (Followers: 5)
Biomedical Microdevices     Hybrid Journal   (Followers: 8)
Biomedical Science and Engineering     Open Access   (Followers: 3)
Biomedizinische Technik - Biomedical Engineering     Hybrid Journal  
Biomicrofluidics     Open Access   (Followers: 4)
BioNanoMaterials     Hybrid Journal   (Followers: 1)
Biotechnology Progress     Hybrid Journal   (Followers: 39)
Boletin Cientifico Tecnico INIMET     Open Access  
Botswana Journal of Technology     Full-text available via subscription  
Boundary Value Problems     Open Access   (Followers: 1)
Brazilian Journal of Science and Technology     Open Access   (Followers: 2)
Broadcasting, IEEE Transactions on     Hybrid Journal   (Followers: 10)
Bulletin of Canadian Petroleum Geology     Full-text available via subscription   (Followers: 14)
Bulletin of Engineering Geology and the Environment     Hybrid Journal   (Followers: 3)
Bulletin of the Crimean Astrophysical Observatory     Hybrid Journal  
Cahiers, Droit, Sciences et Technologies     Open Access  
Calphad     Hybrid Journal  
Canadian Geotechnical Journal     Full-text available via subscription   (Followers: 13)
Canadian Journal of Remote Sensing     Full-text available via subscription   (Followers: 40)
Case Studies in Engineering Failure Analysis     Open Access   (Followers: 7)
Case Studies in Thermal Engineering     Open Access   (Followers: 3)
Catalysis Communications     Hybrid Journal   (Followers: 6)
Catalysis Letters     Hybrid Journal   (Followers: 2)
Catalysis Reviews: Science and Engineering     Hybrid Journal   (Followers: 8)
Catalysis Science and Technology     Free   (Followers: 6)
Catalysis Surveys from Asia     Hybrid Journal   (Followers: 3)
Catalysis Today     Hybrid Journal   (Followers: 5)
CEAS Space Journal     Hybrid Journal  
Cellular and Molecular Neurobiology     Hybrid Journal   (Followers: 3)
Central European Journal of Engineering     Hybrid Journal   (Followers: 1)
CFD Letters     Open Access   (Followers: 6)
Chaos : An Interdisciplinary Journal of Nonlinear Science     Hybrid Journal   (Followers: 2)
Chaos, Solitons & Fractals     Hybrid Journal   (Followers: 3)
Chinese Journal of Catalysis     Full-text available via subscription   (Followers: 2)
Chinese Journal of Engineering     Open Access   (Followers: 2)
Chinese Science Bulletin     Open Access   (Followers: 1)
Ciencia e Ingenieria Neogranadina     Open Access  
Ciencia en su PC     Open Access   (Followers: 1)
Ciencias Holguin     Open Access   (Followers: 1)
CienciaUAT     Open Access  
Cientifica     Open Access  
CIRP Annals - Manufacturing Technology     Full-text available via subscription   (Followers: 11)
CIRP Journal of Manufacturing Science and Technology     Full-text available via subscription   (Followers: 14)
City, Culture and Society     Hybrid Journal   (Followers: 21)
Clay Minerals     Full-text available via subscription   (Followers: 9)
Clean Air Journal     Full-text available via subscription   (Followers: 2)
Coal Science and Technology     Full-text available via subscription   (Followers: 3)
Coastal Engineering     Hybrid Journal   (Followers: 11)
Coastal Engineering Journal     Hybrid Journal   (Followers: 4)
Coatings     Open Access   (Followers: 2)
Cogent Engineering     Open Access   (Followers: 2)
Cognitive Computation     Hybrid Journal   (Followers: 4)
Color Research & Application     Hybrid Journal   (Followers: 1)
COMBINATORICA     Hybrid Journal  
Combustion Theory and Modelling     Hybrid Journal   (Followers: 13)
Combustion, Explosion, and Shock Waves     Hybrid Journal   (Followers: 13)
Communications Engineer     Hybrid Journal   (Followers: 1)
Communications in Numerical Methods in Engineering     Hybrid Journal   (Followers: 2)
Components, Packaging and Manufacturing Technology, IEEE Transactions on     Hybrid Journal   (Followers: 23)
Composite Interfaces     Hybrid Journal   (Followers: 6)
Composite Structures     Hybrid Journal   (Followers: 252)
Composites Part A : Applied Science and Manufacturing     Hybrid Journal   (Followers: 176)
Composites Part B : Engineering     Hybrid Journal   (Followers: 222)
Composites Science and Technology     Hybrid Journal   (Followers: 164)
Comptes Rendus Mécanique     Full-text available via subscription   (Followers: 2)
Computation     Open Access  
Computational Geosciences     Hybrid Journal   (Followers: 12)
Computational Optimization and Applications     Hybrid Journal   (Followers: 7)
Computational Science and Discovery     Full-text available via subscription   (Followers: 2)
Computer Applications in Engineering Education     Hybrid Journal   (Followers: 6)
Computer Science and Engineering     Open Access   (Followers: 17)
Computers & Geosciences     Hybrid Journal   (Followers: 25)
Computers & Mathematics with Applications     Full-text available via subscription   (Followers: 5)
Computers and Electronics in Agriculture     Hybrid Journal   (Followers: 4)
Computers and Geotechnics     Hybrid Journal   (Followers: 8)
Computing and Visualization in Science     Hybrid Journal   (Followers: 6)
Computing in Science & Engineering     Full-text available via subscription   (Followers: 25)
Conciencia Tecnologica     Open Access  
Concurrent Engineering     Hybrid Journal   (Followers: 3)
Continuum Mechanics and Thermodynamics     Hybrid Journal   (Followers: 6)
Control and Dynamic Systems     Full-text available via subscription   (Followers: 8)
Control Engineering Practice     Hybrid Journal   (Followers: 41)
Control Theory and Informatics     Open Access   (Followers: 7)
Corrosion Science     Hybrid Journal   (Followers: 24)
CT&F Ciencia, Tecnologia y Futuro     Open Access  
CTheory     Open Access  

        1 2 3 4 5 6 | Last

Journal Cover Computation
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   ISSN (Online) 2079-3197
   Published by MDPI Homepage  [148 journals]
  • Computation, Vol. 5, Pages 19: Esoteric Twist: An Efficient in-Place
           Streaming Algorithmus for the Lattice Boltzmann Method on Massively
           Parallel Hardware

    • Authors: Martin Geier, Martin Schönherr
      First page: 19
      Abstract: We present and analyze the Esoteric Twist algorithm for the Lattice Boltzmann Method. Esoteric Twist is a thread safe in-place streaming method that combines streaming and collision and requires only a single data set. Compared to other in-place streaming techniques, Esoteric Twist minimizes the memory footprint and the memory traffic when indirect addressing is used. Esoteric Twist is particularly suitable for the implementation of the Lattice Boltzmann Method on Graphic Processing Units.
      PubDate: 2017-03-23
      DOI: 10.3390/computation5020019
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 20: Detecting Perturbed Subpathways towards
           Mouse Lung Regeneration Following H1N1 Influenza Infection

    • Authors: Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Andreas Kanavos, Spyros Sioutas, Athanasios Tsakalidis
      First page: 20
      Abstract: It has already been established by the systems-level approaches that the future of predictive disease biomarkers will not be sketched by plain lists of genes or proteins or other biological entities but rather integrated entities that consider all underlying component relationships. Towards this orientation, early pathway-based approaches coupled expression data with whole pathway interaction topologies but it was the recent approaches that zoomed into subpathways (local areas of the entire biological pathway) that provided more targeted and context-specific candidate disease biomarkers. Here, we explore the application potential of PerSubs, a graph-based algorithm which identifies differentially activated disease-specific subpathways. PerSubs is applicable both for microarray and RNA-Seq data and utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) database as reference for biological pathways. PerSubs operates in two stages: first, identifies differentially expressed genes (or uses any list of disease-related genes) and in second stage, treating each gene of the list as start point, it scans the pathway topology around to build meaningful subpathway topologies. Here, we apply PerSubs to investigate which pathways are perturbed towards mouse lung regeneration following H1N1 influenza infection.
      PubDate: 2017-04-03
      DOI: 10.3390/computation5020020
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 21: An Information Technology Framework for the
           Development of an Embedded Computer System for the Remote and
           Non-Destructive Study of Sensitive Archaeology Sites

    • Authors: Iliya Georgiev, Ivo Georgiev
      First page: 21
      Abstract: The paper proposes an information technology framework for the development of an embedded remote system for non-destructive observation and study of sensitive archaeological sites. The overall concept and motivation are described. The general hardware layout and software configuration are presented. The paper concentrates on the implementation of the following informational technology components: (a) a geographically unique identification scheme supporting a global key space for a key-value store; (b) a common method for octree modeling for spatial geometrical models of the archaeological artifacts, and abstract object representation in the global key space; (c) a broadcast of the archaeological information as an Extensible Markup Language (XML) stream over the Web for worldwide availability; and (d) a set of testing methods increasing the fault tolerance of the system. This framework can serve as a foundation for the development of a complete system for remote archaeological exploration of enclosed archaeological sites like buried churches, tombs, and caves. An archaeological site is opened once upon discovery, the embedded computer system is installed inside upon a robotic platform, equipped with sensors, cameras, and actuators, and the intact site is sealed again. Archaeological research is conducted on a multimedia data stream which is sent remotely from the system and conforms to necessary standards for digital archaeology.
      PubDate: 2017-04-05
      DOI: 10.3390/computation5020021
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 22: Scatter Search Applied to the Inference of
           a Development Gene Network

    • Authors: Amir Abdol, Damjan Cicin-Sain, Jaap Kaandorp, Anton Crombach
      First page: 22
      Abstract: Efficient network inference is one of the challenges of current-day biology. Its application to the study of development has seen noteworthy success, yet a multicellular context, tissue growth, and cellular rearrangements impose additional computational costs and prohibit a wide application of current methods. Therefore, reducing computational cost and providing quick feedback at intermediate stages are desirable features for network inference. Here we propose a hybrid approach composed of two stages: exploration with scatter search and exploitation of intermediate solutions with low temperature simulated annealing. We test the approach on the well-understood process of early body plan development in flies, focusing on the gap gene network. We compare the hybrid approach to simulated annealing, a method of network inference with a proven track record. We find that scatter search performs well at exploring parameter space and that low temperature simulated annealing refines the intermediate results into excellent model fits. From this we conclude that for poorly-studied developmental systems, scatter search is a valuable tool for exploration and accelerates the elucidation of gene regulatory networks.
      PubDate: 2017-05-04
      DOI: 10.3390/computation5020022
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 23: Implicit Large Eddy Simulation of Flow in a
           Micro-Orifice with the Cumulant Lattice Boltzmann Method

    • Authors: Ehsan Kian Far, Martin Geier, Konstantin Kutscher, Manfred Krafczyk
      First page: 23
      Abstract: A detailed numerical study of turbulent flow through a micro-orifice is presented in this work. The flow becomes turbulent due to the orifice at the considered Reynolds numbers (∼ 10 4 ). The obtained flow rates are in good agreement with the experimental measurements. The discharge coefficient and the pressure loss are presented for two input pressures. The laminar stress and the generated turbulent stresses are investigated in detail, and the location of the vena contracta is quantitatively reproduced.
      PubDate: 2017-05-05
      DOI: 10.3390/computation5020023
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 24: Analyzing the Effect and Performance of
           Lossy Compression on Aeroacoustic Simulation of Gas Injector

    • Authors: Seyyed Najmabadi, Philipp Offenhäuser, Moritz Hamann, Guhathakurta Jajnabalkya, Fabian Hempert, Colin Glass, Sven Simon
      First page: 24
      Abstract: Computational fluid dynamic simulations involve large state data, leading to performance degradation due to data transfer times, while requiring large disk space. To alleviate the situation, an adaptive lossy compression algorithm has been developed, which is based on regions of interest. This algorithm uses prediction-based compression and exploits the temporal coherence between subsequent simulation frames. The difference between the actual value and the predicted value is adaptively quantized and encoded. The adaptation is in line with user requirements, that consist of the acceptable inaccuracy, the regions of interest and the required compression throughput. The data compression algorithm was evaluated with simulation data obtained by the discontinuous Galerkin spectral element method. We analyzed the performance, compression ratio and inaccuracy introduced by the lossy compression algorithm. The post processing analysis shows high compression ratios, with reasonable quantization errors.
      PubDate: 2017-05-12
      DOI: 10.3390/computation5020024
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 25: Numerical Simulation of the Laminar Forced
           Convective Heat Transfer between Two Concentric Cylinders

    • Authors: Ioan Sarbu, Anton Iosif
      First page: 25
      Abstract: The dual reciprocity method (DRM) is a highly efficient numerical method of transforming domain integrals arising from the non-homogeneous term of the Poisson equation into equivalent boundary integrals. In this paper, the velocity and temperature fields of laminar forced heat convection in a concentric annular tube, with constant heat flux boundary conditions, have been studied using numerical simulations. The DRM has been used to solve the governing equation, which is expressed in the form of a Poisson equation. A test problem is employed to verify the DRM solutions with different boundary element discretizations and numbers of internal points. The results of the numerical simulations are discussed and compared with exact analytical solutions. Good agreement between the numerical results and exact solutions is evident, as the maximum relative errors are less than 5% to 6%, and the R2-values are greater than 0.999 in all cases. These results confirm the effectiveness and accuracy of the proposed numerical model, which is based on the DRM.
      PubDate: 2017-05-13
      DOI: 10.3390/computation5020025
      Issue No: Vol. 5, No. 2 (2017)
       
  • Computation, Vol. 5, Pages 4: An SVM Framework for Malignant Melanoma
           Detection Based on Optimized HOG Features

    • Authors: Samy Bakheet
      First page: 4
      Abstract: Early detection of skin cancer through improved techniques and innovative technologies has the greatest potential for significantly reducing both morbidity and mortality associated with this disease. In this paper, an effective framework of a CAD (Computer-Aided Diagnosis) system for melanoma skin cancer is developed mainly by application of an SVM (Support Vector Machine) model on an optimized set of HOG (Histogram of Oriented Gradient) based descriptors of skin lesions. Experimental results obtained by applying the presented methodology on a large, publicly accessible dataset of dermoscopy images demonstrate that the proposed framework is a strong contender for the state-of-the-art alternatives by achieving high levels of sensitivity, specificity, and accuracy (98.21%, 96.43% and 97.32%, respectively), without sacrificing computational soundness.
      PubDate: 2017-01-01
      DOI: 10.3390/computation5010004
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 5: First Principle Modelling of Materials and
           Processes in Dye-Sensitized Photoanodes for Solar Energy and Solar Fuels

    • Authors: Mariachiara Pastore
      First page: 5
      Abstract: In the context of solar energy exploitation, dye-sensitized solar cells and dye-sensitized photoelectrosynthetic cells offer the promise of low-cost sunlight conversion and storage, respectively. In this perspective we discuss the main successes and limitations of modern computational methodologies, ranging from hybrid and long-range corrected density functionals, GW approaches and multi-reference perturbation theories, in describing the electronic and optical properties of isolated components and complex interfaces relevant to these devices. While computational modelling has had a crucial role in the development of the dye-sensitized solar cells technology, the theoretical characterization of the interface structure and interfacial processes in water splitting devices is still at its infancy, especially concerning the electron and hole transfer phenomena. Quantitative analysis of interfacial charge separation and recombination reactions in multiple metal-oxide/dye/catalyst heterointerfaces, thus, undoubtedly represents the compelling challenge in the field of modern computational material science.
      PubDate: 2017-01-01
      DOI: 10.3390/computation5010005
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 6: Towards a Multiscale Model of Acute HIV
           Infection

    • Authors: Anass Bouchnita, Gennady Bocharov, Andreas Meyerhans, Vitaly Volpert
      First page: 6
      Abstract: Human Immunodeficiency Virus (HIV) infection of humans represents a complex biological system and a great challenge to public health. Novel approaches for the analysis and prediction of the infection dynamics based on a multi-scale integration of virus ontogeny and immune reactions are needed to deal with the systems’ complexity. The aim of our study is: (1) to formulate a multi-scale mathematical model of HIV infection; (2) to implement the model computationally following a hybrid approach; and (3) to calibrate the model by estimating the parameter values enabling one to reproduce the “standard” observed dynamics of HIV infection in blood during the acute phase of primary infection. The modeling approach integrates the processes of infection spread and immune responses in Lymph Nodes (LN) to that observed in blood. The spatio-temporal population dynamics of T lymphocytes in LN in response to HIV infection is governed by equations linking an intracellular regulation of the lymphocyte fate by intercellular cytokine fields. We describe the balance of proliferation, differentiation and death at a single cell level as a consequence of gene activation via multiple signaling pathways activated by IL-2, IFNa and FasL. Distinct activation thresholds are used in the model to relate different modes of cellular responses to the hierarchy of the relative levels of the cytokines. We specify a reference set of model parameter values for the fundamental processes in lymph nodes that ensures a reasonable agreement with viral load and CD4+ T cell dynamics in blood.
      PubDate: 2017-01-10
      DOI: 10.3390/computation5010006
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 7: Acknowledgement to Reviewers of Computation
           in 2016

    • Authors: Computation Editorial Office
      First page: 7
      Abstract: The editors of Computation would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016.[...]
      PubDate: 2017-01-10
      DOI: 10.3390/computation5010007
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 8: Numerical and Computational Analysis of a
           New Vertical Axis Wind Turbine, Named KIONAS

    • Authors: Eleni Douvi, Dimitra Douvi, Dionissios Margaris, Ioannis Drosis
      First page: 8
      Abstract: This paper concentrates on a new configuration for a wind turbine, named KIONAS. The main purpose is to determine the performance and aerodynamic behavior of KIONAS, which is a vertical axis wind turbine with a stator over the rotor and a special feature in that it can consist of several stages. Notably, the stator is shaped in such a way that it increases the velocity of the air impacting the rotor blades. Moreover, each stage’s performance can be increased with the increase of the total number of stages. The effects of wind velocity, the various numbers of inclined rotor blades, the rotor diameter, the stator’s shape and the number of stages on the performance of KIONAS were studied. A FORTRAN code was developed in order to predict the power in several cases by solving the equations of continuity and momentum. Subsequently, further knowledge on the flow field was obtained by using a commercial Computational Fluid Dynamics code. Based on the results, it can be concluded that higher wind velocities and a greater number of blades produce more power. Furthermore, higher performance was found for a stator with curved guide vanes and for a KIONAS configuration with more stages.
      PubDate: 2017-01-11
      DOI: 10.3390/computation5010008
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 9: Excitons in Solids from Time-Dependent
           Density-Functional Theory: Assessing the Tamm-Dancoff Approximation

    • Authors: Young-Moo Byun, Carsten Ullrich
      First page: 9
      Abstract: Excitonic effects in solids can be calculated using the Bethe-Salpeter equation (BSE) or the Casida equation of time-dependent density-functional theory (TDDFT). In both methods, the Tamm-Dancoff approximation (TDA), which decouples excitations and de-excitations, is widely used to reduce computational cost. Here, we study the effect of the TDA on exciton binding energies of solids obtained from the Casida equation using long-range-corrected (LRC) exchange-correlation kernels. We find that the TDA underestimates TDDFT-LRC exciton binding energies of semiconductors slightly, but those of insulators significantly (i.e., by more than 100%), and thus it is essential to solve the full Casida equation to describe strongly bound excitons. These findings are relevant in the ongoing search for accurate and efficient TDDFT approaches for excitons.
      PubDate: 2017-01-29
      DOI: 10.3390/computation5010009
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 10: Virtual Prototyping and Validation of Cpps
           within a New Software Framework

    • Authors: Sebastian Neumeyer, Konrad Exner, Simon Kind, Haygazun Hayka, Rainer Stark
      First page: 10
      Abstract: As a result of the growing demand for highly customized and individual products, companies need to enable flexible and intelligent manufacturing. Cyber-physical production systems (CPPS) will act autonomously in the future in an interlinked production and enable such flexibility. However, German mid-sized plant manufacturers rarely use virtual technologies for design and validation in order to design CPPS. The research project Virtual Commissioning with Smart Hybrid Prototyping (VIB-SHP) investigated the usage of virtual technologies for manufacturing systems and CPPS design. Aspects of asynchronous communicating, intelligent- and autonomous-acting production equipment in an immersive validation environment, have been investigated. To enable manufacturing system designers to validate CPPS, a software framework for virtual prototyping has been developed. A mechatronic construction kit for production system design integrates discipline-specific models and manages them in a product lifecycle management (PLM) solution. With this construction kit manufacturing designers are able to apply virtual technologies and the validation of communication processes with the help of behavior models. The presented approach resolves the sequential design process for the development of mechanical, electrical, and software elements and ensures the consistency of these models. With the help of a bill of material (BOM)- and signal-based alignment of the discipline-specific models in an integrated mechatronic product model, the communication of the design status and changes are improved. The re-use of already-specified and -designed modules enable quick behavior modeling, code evaluation, as well as interaction with the virtualized assembly system in an immersive environment.
      PubDate: 2017-02-18
      DOI: 10.3390/computation5010010
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 11: Multiscale CT-Based Computational Modeling
           of Alveolar Gas Exchange during Artificial Lung Ventilation, Cluster
           (Biot) and Periodic (Cheyne-Stokes) Breathings and Bronchial Asthma Attack
           

    • Authors: Andrey Golov, Sergey Simakov, Yan Soe, Roman Pryamonosov, Ospan Mynbaev, Alexander Kholodov
      First page: 11
      Abstract: An airflow in the first four generations of the tracheobronchial tree was simulated by the 1D model of incompressible fluid flow through the network of the elastic tubes coupled with 0D models of lumped alveolar components, which aggregates parts of the alveolar volume and smaller airways, extended with convective transport model throughout the lung and alveolar components which were combined with the model of oxygen and carbon dioxide transport between the alveolar volume and the averaged blood compartment during pathological respiratory conditions. The novel features of this work are 1D reconstruction of the tracheobronchial tree structure on the basis of 3D segmentation of the computed tomography (CT) data; 1D−0D coupling of the models of 1D bronchial tube and 0D alveolar components; and the alveolar gas exchange model. The results of our simulations include mechanical ventilation, breathing patterns of severely ill patients with the cluster (Biot) and periodic (Cheyne-Stokes) respirations and bronchial asthma attack. The suitability of the proposed mathematical model was validated. Carbon dioxide elimination efficiency was analyzed in all these cases. In the future, these results might be integrated into research and practical studies aimed to design cyberbiological systems for remote real-time monitoring, classification, prediction of breathing patterns and alveolar gas exchange for patients with breathing problems.
      PubDate: 2017-02-18
      DOI: 10.3390/computation5010011
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 12: Numerical Modelling of Double-Steel Plate
           Composite Shear Walls

    • Authors: Michaela Elmatzoglou, Aris Avdelas
      First page: 12
      Abstract: Double-steel plate concrete composite shear walls are being used for nuclear plants and high-rise buildings. They consist of thick concrete walls, exterior steel faceplates serving as reinforcement and shear connectors, which guarantee the composite action between the two different materials. Several researchers have used the Finite Element Method to investigate the behaviour of double-steel plate concrete walls. The majority of them model every element explicitly leading to a rather time-consuming solution, which cannot be easily used for design purposes. In the present paper, the main objective is the introduction of a three-dimensional finite element model, which can efficiently predict the overall performance of a double-steel plate concrete wall in terms of accuracy and time saving. At first, empirical formulations and design relations established in current design codes for shear connectors are evaluated. Then, a simplified finite element model is used to investigate the nonlinear response of composite walls. The developed model is validated using results from tests reported in the literature in terms of axial compression and monotonic, cyclic in-plane shear loading. Several finite element modelling issues related to potential convergence problems, loading strategies and computer efficiency are also discussed. The accuracy and simplicity of the proposed model make it suitable for further numerical studies on the shear connection behaviour at the steel-concrete interface.
      PubDate: 2017-02-22
      DOI: 10.3390/computation5010012
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 13: Aerodynamic Performance of a NREL S809
           Airfoil in an Air-Sand Particle Two-Phase Flow

    • Authors: Dimitra Douvi, Dionissios Margaris, Aristeidis Davaris
      First page: 13
      Abstract: This paper opens up a new perspective on the aerodynamic performance of a wind turbine airfoil. More specifically, the paper deals with a steady, incompressible two-phase flow, consisting of air and two different concentrations of sand particles, over an airfoil from the National Renewable Energy Laboratory, NREL S809. The numerical simulations were performed on turbulence models for aerodynamic operations using commercial computational fluid dynamics (CFD) code. The computational results obtained for the aerodynamic performance of an S809 airfoil at various angles of attack operating at Reynolds numbers of Re = 1 × 106 and Re = 2 × 106 in a dry, dusty environment were compared with existing experimental data on air flow over an S809 airfoil from reliable sources. Notably, a structured mesh consisting of 80,000 cells had already been identified as the most appropriate for numerical simulations. Finally, it was concluded that sand concentration significantly affected the aerodynamic performance of the airfoil; there was an increase in the values of the predicted drag coefficients, as well as a decrease in the values of the predicted lift coefficients caused by increasing concentrations of sand particles. The region around the airfoil was studied by using contours of static pressure and discrete phase model (DPM) concentration.
      PubDate: 2017-02-28
      DOI: 10.3390/computation5010013
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 14: Simplification of Reaction Networks,
           Confluence and Elementary Modes

    • Authors: Guillaume Madelaine, Elisa Tonello, Cédric Lhoussaine, Joachim Niehren
      First page: 14
      Abstract: Reaction networks can be simplified by eliminating linear intermediate species in partial steadystates. Inthispaper,westudythequestionwhetherthisrewriteprocedureisconfluent,so that for any given reaction network with kinetic constraints, a unique normal form will be obtained independently of the elimination order. We first show that confluence fails for the elimination of intermediates even without kinetics, if “dependent reactions” introduced by the simplification are not removed. This leads us to revising the simplification algorithm into a variant of the double description method for computing elementary modes, so that it keeps track of kinetic information. Folklore results on elementary modes imply the confluence of the revised simplification algorithm with respect to the network structure, i.e., the structure of fully simplified networks is unique. We show, however, that the kinetic rates assigned to the reactions may not be unique, and provide a biological example where two different simplified networks can be obtained. Finally, we give a criterion on the structure of the initial network that is sufficient to guarantee the confluence of both the structure and the kinetic rates.
      PubDate: 2017-03-10
      DOI: 10.3390/computation5010014
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 15: Schrödinger Theory of Electrons in
           Electromagnetic Fields: New Perspectives

    • Authors: Viraht Sahni, Xiao-Yin Pan
      First page: 15
      Abstract: The Schrödinger theory of electrons in an external electromagnetic field is described from the new perspective of the individual electron. The perspective is arrived at via the time-dependent “Quantal Newtonian” law (or differential virial theorem). (The time-independent law, a special case, provides a similar description of stationary-state theory). These laws are in terms of “classical” fields whose sources are quantal expectations of Hermitian operators taken with respect to the wave function. The laws reveal the following physics: (a) in addition to the external field, each electron experiences an internal field whose components are representative of a specific property of the system such as the correlations due to the Pauli exclusion principle and Coulomb repulsion, the electron density, kinetic effects, and an internal magnetic field component. The response of the electron is described by the current density field; (b) the scalar potential energy of an electron is the work done in a conservative field. It is thus path-independent. The conservative field is the sum of the internal and Lorentz fields. Hence, the potential is inherently related to the properties of the system, and its constituent property-related components known. As the sources of the fields are functionals of the wave function, so are the respective fields, and, therefore, the scalar potential is a known functional of the wave function; (c) as such, the system Hamiltonian is a known functional of the wave function. This reveals the intrinsic self-consistent nature of the Schrödinger equation, thereby providing a path for the determination of the exact wave functions and energies of the system; (d) with the Schrödinger equation written in self-consistent form, the Hamiltonian now admits via the Lorentz field a new term that explicitly involves the external magnetic field. The new understandings are explicated for the stationary state case by application to two quantum dots in a magnetostatic field, one in a ground state and the other in an excited state. For the time-dependent case, the evolution of the same states of the quantum dots in both a magnetostatic and a time-dependent electric field is described. In each case, the satisfaction of the corresponding “Quantal Newtonian” law is demonstrated.
      PubDate: 2017-03-09
      DOI: 10.3390/computation5010015
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 16: A Hybrid Computation Model to Describe the
           Progression of Multiple Myeloma and Its Intra-Clonal Heterogeneity

    • Authors: Anass Bouchnita, Fatima-Ezzahra Belmaati, Rajae Aboulaich, Mark Koury, Vitaly Volpert
      First page: 16
      Abstract: Multiplemyeloma(MM)isageneticallycomplexhematologicalcancerthatischaracterized by proliferation of malignant plasma cells in the bone marrow. MM evolves from the clonal premalignant disorder monoclonal gammopathy of unknown significance (MGUS) by sequential genetic changes involving many different genes, resulting in dysregulated growth of multiple clones of plasma cells. The migration, survival, and proliferation of these clones require the direct and indirect interactions with the non-hematopoietic cells of the bone marrow. We develop a hybrid discrete-continuous model of MM development from the MGUS stage. The discrete aspect of the modelisobservedatthecellularlevel: cellsarerepresentedasindividualobjectswhichmove,interact, divide, and die by apoptosis. Each of these actions is regulated by intracellular and extracellular processes as described by continuous models. The hybrid model consists of the following submodels that have been simplified from the much more complex state of evolving MM: cell motion due to chemotaxis, intracellular regulation of plasma cells, extracellular regulation in the bone marrow, and acquisition of mutations upon cell division. By extending a previous, simpler model in which the extracellular matrix was considered to be uniformly distributed, the new hybrid model provides a more accurate description in which cytokines are produced by the marrow microenvironment and consumed by the myeloma cells. The complex multiple genetic changes in MM cells and the numerous cell-cell and cytokine-mediated interactions between myeloma cells and their marrow microenviroment are simplified in the model such that four related but evolving MM clones can be studied as they compete for dominance in the setting of intraclonal heterogeneity.
      PubDate: 2017-03-10
      DOI: 10.3390/computation5010016
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 17: Evaluation of Soil-Structure Interaction on
           the Seismic Response of Liquid Storage Tanks under Earthquake Ground
           Motions

    • Authors: Mostafa Farajian, Mohammad Khodakarami, Denise-Penelope Kontoni
      First page: 17
      Abstract: Soil-structure interaction (SSI) could affect the seismic response of structures. Since liquid storage tanks are vital structures and must continue their operation under severe earthquakes, their seismic behavior should be studied. Accordingly, the seismic response of two types of steel liquid storage tanks (namely, broad and slender, with aspect ratios of height to radius equal to 0.6 and 1.85) founded on half-space soil is scrutinized under different earthquake ground motions. For a better comparison, the six considered ground motions are classified, based on their pulse-like characteristics, into two groups, named far and near fault ground motions. To model the liquid storage tanks, the simplified mass-spring model is used and the liquid is modeled as two lumped masses known as sloshing and impulsive, and the interaction of fluid and structure is considered using two coupled springs and dashpots. The SSI effect, also, is considered using a coupled spring and dashpot. Additionally, four types of soils are used to consider a wide variety of soil properties. To this end, after deriving the equations of motion, MATLAB programming is employed to obtain the time history responses. Results show that although the SSI effect leads to a decrease in the impulsive displacement, overturning moment, and normalized base shear, the sloshing (or convective) displacement is not affected by such effects due to its long period.
      PubDate: 2017-03-12
      DOI: 10.3390/computation5010017
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 18: An Accurate Computational Tool for
           Performance Estimation of FSO Communication Links over Weak to Strong
           Atmospheric Turbulent Channels

    • Authors: Theodore D. Katsilieris, George P. Latsas, Hector E. Nistazakis, George S. Tombras
      First page: 18
      Abstract: The terrestrial optical wireless communication links have attracted significant research and commercial worldwide interest over the last few years due to the fact that they offer very high and secure data rate transmission with relatively low installation and operational costs, and without need of licensing. However, since the propagation path of the information signal, i.e., the laser beam, is the atmosphere, their effectivity affects the atmospheric conditions strongly in the specific area. Thus, system performance depends significantly on the rain, the fog, the hail, the atmospheric turbulence, etc. Due to the influence of these effects, it is necessary to study, theoretically and numerically, very carefully before the installation of such a communication system. In this work, we present exactly and accurately approximate mathematical expressions for the estimation of the average capacity and the outage probability performance metrics, as functions of the link’s parameters, the transmitted power, the attenuation due to the fog, the ambient noise and the atmospheric turbulence phenomenon. The latter causes the scintillation effect, which results in random and fast fluctuations of the irradiance at the receiver’s end. These fluctuations can be studied accurately with statistical methods. Thus, in this work, we use either the lognormal or the gamma–gamma distribution for weak or moderate to strong turbulence conditions, respectively. Moreover, using the derived mathematical expressions, we design, accomplish and present a computational tool for the estimation of these systems’ performances, while also taking into account the parameter of the link and the atmospheric conditions. Furthermore, in order to increase the accuracy of the presented tool, for the cases where the obtained analytical mathematical expressions are complex, the performance results are verified with the numerical estimation of the appropriate integrals. Finally, using the derived mathematical expression and the presented computational tool, we present the corresponding numerical results, using common parameter values for realistic terrestrial free space optical communication systems.
      PubDate: 2017-03-18
      DOI: 10.3390/computation5010018
      Issue No: Vol. 5, No. 1 (2017)
       
  • Computation, Vol. 5, Pages 1: Application of the Recursive Finite Element
           Approach on 2D Periodic Structures under Harmonic Vibrations

    • Authors: Reem Yassine, Faten Salman, Ali Al Shaer, Mohammad Hammoud, Denis Duhamel
      First page: 1
      Abstract: The frequency response function is a quantitative measure used in structural analysis and engineering design; hence, it is targeted for accuracy. For a large structure, a high number of substructures, also called cells, must be considered, which will lead to a high amount of computational time. In this paper, the recursive method, a finite element method, is used for computing the frequency response function, independent of the number of cells with much lesser time costs. The fundamental principle is eliminating the internal degrees of freedom that are at the interface between a cell and its succeeding one. The method is applied solely for free (no load) nodes. Based on the boundary and interior degrees of freedom, the global dynamic stiffness matrix is computed by means of products and inverses resulting with a dimension the same as that for one cell. The recursive method is demonstrated on periodic structures (cranes and buildings) under harmonic vibrations. The method yielded a satisfying time decrease with a maximum time ratio of 1 18 and a percentage difference of 19%, in comparison with the conventional finite element method. Close values were attained at low and very high frequencies; the analysis is supported for two types of materials (steel and plastic). The method maintained its efficiency with a high number of forces, excluding the case when all of the nodes are under loads.
      PubDate: 2016-12-22
      DOI: 10.3390/computation5010001
      Issue No: Vol. 5, No. 1 (2016)
       
  • Computation, Vol. 5, Pages 2: Power Conversion Efficiency of Arylamine
           Organic Dyes for Dye-Sensitized Solar Cells (DSSCs) Explicit to Cobalt
           Electrolyte: Understanding the Structural Attributes Using a Direct QSPR
           Approach

    • Authors: Supratik Kar, Juganta Roy, Danuta Leszczynska, Jerzy Leszczynski
      First page: 2
      Abstract: Post silicon solar cell era involves light-absorbing dyes for dye-sensitized solar systems (DSSCs). Therefore, there is great interest in the design of competent organic dyes for DSSCs with high power conversion efficiency (PCE) to bypass some of the disadvantages of silicon-based solar cell technologies, such as high cost, heavy weight, limited silicon resources, and production methods that lead to high environmental pollution. The DSSC has the unique feature of a distance-dependent electron transfer step. This depends on the relative position of the sensitized organic dye in the metal oxide composite system. In the present work, we developed quantitative structure-property relationship (QSPR) models to set up the quantitative relationship between the overall PCE and quantum chemical molecular descriptors. They were calculated from density functional theory (DFT) and time-dependent DFT (TD-DFT) methods as well as from DRAGON software. This allows for understanding the basic electron transfer mechanism along with the structural attributes of arylamine-organic dye sensitizers for the DSSCs explicit to cobalt electrolyte. The identified properties and structural fragments are particularly valuable for guiding time-saving synthetic efforts for development of efficient arylamine organic dyes with improved power conversion efficiency.
      PubDate: 2016-12-23
      DOI: 10.3390/computation5010002
      Issue No: Vol. 5, No. 1 (2016)
       
  • Computation, Vol. 5, Pages 3: Critical Issues in Modelling Lymph Node
           Physiology

    • Authors: Dmitry Grebennikov, Raoul van Loon, Mario Novkovic, Lucas Onder, Rostislav Savinkov, Igor Sazonov, Rufina Tretyakova, Daniel Watson, Gennady Bocharov
      First page: 3
      Abstract: In this study, we discuss critical issues in modelling the structure and function of lymph nodes (LNs), with emphasis on how LN physiology is related to its multi-scale structural organization. In addition to macroscopic domains such as B-cell follicles and the T cell zone, there are vascular networks which play a key role in the delivery of information to the inner parts of the LN, i.e., the conduit and blood microvascular networks. We propose object-oriented computational algorithms to model the 3D geometry of the fibroblastic reticular cell (FRC) network and the microvasculature. Assuming that a conduit cylinder is densely packed with collagen fibers, the computational flow study predicted that the diffusion should be a dominating process in mass transport than convective flow. The geometry models are used to analyze the lymph flow properties through the conduit network in unperturbed- and damaged states of the LN. The analysis predicts that elimination of up to 60%–90% of edges is required to stop the lymph flux. This result suggests a high degree of functional robustness of the network.
      PubDate: 2016-12-24
      DOI: 10.3390/computation5010003
      Issue No: Vol. 5, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 38: Steady-State Anderson Accelerated Coupling
           of Lattice Boltzmann and Navier–Stokes Solvers

    • Authors: Atanas Atanasov, Benjamin Uekermann, Carlos Pachajoa Mejía, Hans-Joachim Bungartz, Philipp Neumann
      First page: 38
      Abstract: We present an Anderson acceleration-based approach to spatially couple three-dimensional Lattice Boltzmann and Navier–Stokes (LBNS) flow simulations. This allows to locally exploit the computational features of both fluid flow solver approaches to the fullest extent and yields enhanced control to match the LB and NS degrees of freedom within the LBNS overlap layer. Designed for parallel Schwarz coupling, the Anderson acceleration allows for the simultaneous execution of both Lattice Boltzmann and Navier–Stokes solver. We detail our coupling methodology, validate it, and study convergence and accuracy of the Anderson accelerated coupling, considering three steady-state scenarios: plane channel flow, flow around a sphere and channel flow across a porous structure. We find that the Anderson accelerated coupling yields a speed-up (in terms of iteration steps) of up to 40% in the considered scenarios, compared to strictly sequential Schwarz coupling.
      PubDate: 2016-10-17
      DOI: 10.3390/computation4040038
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 39: A Multi-Compartment Hybrid Computational
           Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection

    • Authors: Simeone Marino, Denise Kirschner
      First page: 39
      Abstract: Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs), take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung) to lung-draining lymph nodes (LNs) where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim) describing in silico immune cell, bacterial (Mtb) and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form), lung draining lymph node (LN, site of generation of adaptive immunity) and blood (a measurable compartment). Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM), while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs). In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs) in a computational fashion into GranSim. Results: The model was calibrated using experimental data from the lungs and blood of NHPs. The addition of DCs allowed us to investigate in greater detail mechanisms of recruitment, trafficking and antigen presentation and their role in tuberculosis infection. Conclusion: The main conclusion of this study is that early events after Mtb infection are critical to establishing a timely and effective response. Manipulating CD8+ and CD4+ T cell proliferation rates, as well as DC migration early on during infection can determine the difference between bacterial clearance vs. uncontrolled bacterial growth and dissemination.
      PubDate: 2016-10-21
      DOI: 10.3390/computation4040039
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 40: Obituary for Walter Kohn (1923–2016)

    • Authors: Karlheinz Schwarz, Lu Sham, Ann Mattsson, Matthias Scheffler
      First page: 40
      Abstract: Walter Kohn (Figure 1) is one of the most cited scientists of our time, who died on 19 April 2016 in Santa Barbara, CA, USA. [...]
      PubDate: 2016-10-20
      DOI: 10.3390/computation4040040
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 41: Evaluation of External Memory Access
           Performance on a High-End FPGA Hybrid Computer

    • Authors: Konstantinos Kalaitzis, Evripidis Sotiriadis, Ioannis Papaefstathiou, Apostolos Dollas
      First page: 41
      Abstract: The motivation of this research was to evaluate the main memory performance of a hybrid super computer such as the Convey HC-x, and ascertain how the controller performs in several access scenarios, vis-à-vis hand-coded memory prefetches. Such memory patterns are very useful in stencil computations. The theoretical bandwidth of the memory of the Convey is compared with the results of our measurements. The accurate study of the memory subsystem is particularly useful for users when they are developing their application-specific personality. Experiments were performed to measure the bandwidth between the coprocessor and the memory subsystem. The experiments aimed mainly at measuring the reading access speed of the memory from Application Engines (FPGAs). Different ways of accessing data were used in order to find the most efficient way to access memory. This way was proposed for future work in the Convey HC-x. When performing a series of accesses to memory, non-uniform latencies occur. The Memory Controller of the Convey HC-x in the coprocessor attempts to cover this latency. We measure memory efficiency as a ratio of the number of memory accesses and the number of execution cycles. The result of this measurement converges to one in most cases. In addition, we performed experiments with hand-coded memory accesses. The analysis of the experimental results shows how the memory subsystem and Memory Controllers work. From this work we conclude that the memory controllers do an excellent job, largely because (transparently to the user) they seem to cache large amounts of data, and hence hand-coding is not needed in most situations.
      PubDate: 2016-10-25
      DOI: 10.3390/computation4040041
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 42: A Mathematical Spline-Based Model of
           Cardiac Left Ventricle Anatomy and Morphology

    • Authors: Sergei Pravdin
      First page: 42
      Abstract: Computer simulation of normal and diseased human heart activity requires a 3D anatomical model of the myocardium, including myofibers. For clinical applications, such a model has to be constructed based on routine methods of cardiac visualization, such as sonography. Symmetrical models are shown to be too rigid, so an analytical non-symmetrical model with enough flexibility is necessary. Based on previously-made anatomical models of the left ventricle, we propose a new, much more flexible spline-based analytical model. The model is fully described and verified against DT-MRI data. We show a way to construct it on the basis of sonography data. To use this model in further physiological simulations, we propose a numerical method to utilize finite differences in solving the reaction-diffusion problem together with an example of scroll wave dynamics simulation.
      PubDate: 2016-10-27
      DOI: 10.3390/computation4040042
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 43: A Theoretical Study of One- and Two-Photon
           Activity of D-Luciferin

    • Authors: Mausumi Chattopadhyaya, Md. Alam
      First page: 43
      Abstract: In the present work, we have theoretically studied the one and two-photon absorption (OPA and TPA) probabilities of the native D-luciferin molecule and attempted to find the origin of its larger TPA cross-sections in polar solvents than in non-polar ones. The calculations using state-of-the-art linear and quadratic response theory in the framework of time-dependent density functional theory using hybrid B3LYP functional and cc-pVDZ basis set suggests that two-photon transition probability of this molecule increases with increasing solvent polarity. In order to explicate our present findings, we employed the generalized few-state-model and inspected the role of different optical channels related to the TPA process. We have found that the two-photon transition probability is always guided by a destructive interference term, the magnitude of which decreases with increasing solvent polarity. Furthermore, we have evaluated OPA parameters of D-luciferin and noticed that the the excitation energy is in very good agreement with the available experimental results.
      PubDate: 2016-11-17
      DOI: 10.3390/computation4040043
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 44: Mathematical Model of a
           Lithium-Bromide/Water Absorption Refrigeration System Equipped with an
           Adiabatic Absorber

    • Authors: Salem Osta-Omar, Christopher Micallef
      First page: 44
      Abstract: The objective of this paper is to develop a mathematical model for thermodynamic analysis of an absorption refrigeration system equipped with an adiabatic absorber using a lithium-bromide/water (LiBr/water) pair as the working fluid. The working temperature of the generator, adiabatic absorber, condenser, evaporator, the cooling capacity of the system, and the ratio of the solution mass flow rate at the circulation pump to that at the solution pump are used as input data. The model evaluates the thermodynamic properties of all state points, the heat transfer in each component, the various mass flow rates, and the coefficient of performance (COP) of the cycle. The results are used to investigate the effect of key parameters on the overall performance of the system. For instance, increasing the generator temperatures and decreasing the adiabatic absorber temperatures can increase the COP of the cycle. The results of this mathematical model can be used for designing and sizing new LiBr/water absorption refrigeration systems equipped with an adiabatic absorber or for optimizing existing aforementioned systems.
      PubDate: 2016-11-17
      DOI: 10.3390/computation4040044
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 45: Special Issue “50th Anniversary of the
           Kohn–Sham Theory—Advances in Density Functional Theory”

    • Authors: Ágnes Nagy, Karlheinz Schwarz
      First page: 45
      Abstract: The properties of many materials at the atomic scale depend on the electronic structure, which requires a quantum mechanical treatment. The most widely used approach to make such a treatment feasible is density functional theory (DFT), the advances in which were presented and discussed during the DFT conference in Debrecen. Some of these issues are presented in this Special Issue.
      PubDate: 2016-11-22
      DOI: 10.3390/computation4040045
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 46: Effect of Pore Structure on Soot Deposition
           in Diesel Particulate Filter

    • Authors: Kazuhiro Yamamoto, Tatsuya Sakai
      First page: 46
      Abstract: Nowadays, in the after-treatment of diesel exhaust gas, a diesel particulate filter (DPF) has been used to trap nano-particles of the diesel soot. However, as there are more particles inside the filter, the pressure which corresponds to the filter backpressure increases, which worsens the fuel consumption rate, together with the abatement of the available torque. Thus, a filter with lower backpressure would be needed. To achieve this, it is necessary to utilize the information on the phenomena including both the soot transport and its removal inside the DPF, and optimize the filter substrate structure. In this paper, to obtain useful information for optimization of the filter structure, we tested seven filters with different porosities and pore sizes. The porosity and pore size were changed systematically. To consider the soot filtration, the particle-laden flow was simulated by a lattice Boltzmann method (LBM). Then, the flow field and the pressure change were discussed during the filtration process.
      PubDate: 2016-12-02
      DOI: 10.3390/computation4040046
      Issue No: Vol. 4, No. 4 (2016)
       
  • Computation, Vol. 4, Pages 23: Orbital Energy-Based Reaction Analysis of
           SN2 Reactions

    • Authors: Takao Tsuneda, Satoshi Maeda, Yu Harabuchi, Raman Singh
      First page: 23
      Abstract: An orbital energy-based reaction analysis theory is presented as an extension of the orbital-based conceptual density functional theory. In the orbital energy-based theory, the orbitals contributing to reactions are interpreted to be valence orbitals giving the largest orbital energy variation from reactants to products. Reactions are taken to be electron transfer-driven when they provide small variations for the gaps between the contributing occupied and unoccupied orbital energies on the intrinsic reaction coordinates in the initial processes. The orbital energy-based theory is then applied to the calculations of several S N 2 reactions. Using a reaction path search method, the Cl− + CH3I → ClCH3 + I− reaction, for which another reaction path called “roundabout path” is proposed, is found to have a precursor process similar to the roundabout path just before this SN2 reaction process. The orbital energy-based theory indicates that this precursor process is obviously driven by structural change, while the successor SN2 reaction proceeds through electron transfer between the contributing orbitals. Comparing the calculated results of the SN2 reactions in gas phase and in aqueous solution shows that the contributing orbitals significantly depend on solvent effects and these orbitals can be correctly determined by this theory.
      PubDate: 2016-07-08
      DOI: 10.3390/computation4030023
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 24: On the v-Representabilty Problem in Density
           Functional Theory: Application to Non-Interacting Systems

    • Authors: Markus Däne, Antonios Gonis
      First page: 24
      Abstract: Based on a computational procedure for determining the functional derivative with respect to the density of any antisymmetric N-particle wave function for a non-interacting system that leads to the density, we devise a test as to whether or not a wave function known to lead to a given density corresponds to a solution of a Schrödinger equation for some potential. We examine explicitly the case of non-interacting systems described by Slater determinants. Numerical examples for the cases of a one-dimensional square-well potential with infinite walls and the harmonic oscillator potential illustrate the formalism.
      PubDate: 2016-07-05
      DOI: 10.3390/computation4030024
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 25: Predictions of Physicochemical Properties
           of Ionic Liquids with DFT

    • Authors: Karl Karu, Anton Ruzanov, Heigo Ers, Vladislav Ivaništšev, Isabel Lage-Estebanez, José García de la Vega
      First page: 25
      Abstract: Nowadays, density functional theory (DFT)-based high-throughput computational approach is becoming more efficient and, thus, attractive for finding advanced materials for electrochemical applications. In this work, we illustrate how theoretical models, computational methods, and informatics techniques can be put together to form a simple DFT-based throughput computational workflow for predicting physicochemical properties of room-temperature ionic liquids. The developed workflow has been used for screening a set of 48 ionic pairs and for analyzing the gathered data. The predicted relative electrochemical stabilities, ionic charges and dynamic properties of the investigated ionic liquids are discussed in the light of their potential practical applications.
      PubDate: 2016-07-19
      DOI: 10.3390/computation4030025
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 26: Interaction of Hydrogen with Au Modified by
           Pd and Rh in View of Electrochemical Applications

    • Authors: Fernanda Juarez, German Soldano, Elizabeth Santos, Hazar Guesmi, Frederik Tielens, Tzonka Mineva
      First page: 26
      Abstract: Hydrogen interaction with bimetallic Au(Pd) and Au(Rh) systems are studied with the density functional theory (DFT)-based periodic approach. Several bimetallic configurations with varying concentrations of Pd and Rh atoms in the under layer of a gold surface(111) were considered. The reactivity of the doped Au(111) toward hydrogen adsorption and absorption was related to the property modifications induced by the presence of metal dopants. DFT-computed quantities, such as the energy stability, the inter-atomic and inter-slab binding energies between gold and dopants, and the charge density were used to infer the similarities and differences between both Pd and Rh dopants in these model alloys. The hydrogen penetration into the surface is favored in the bimetallic slab configurations. The underlayer dopants affect the reactivity of the surface gold toward hydrogen adsorption in the systems with a dopant underlayer, covered by absorbed hydrogen up to a monolayer. This indicates a possibility to tune the gold surface properties of bimetallic electrodes by modulating the degree of hydrogen coverage of the inner dopant layer(s).
      PubDate: 2016-07-20
      DOI: 10.3390/computation4030026
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 27: Automatic Generation of Massively Parallel
           Codes from ExaSlang

    • Authors: Sebastian Kuckuk, Harald Köstler
      First page: 27
      Abstract: Domain-specific languages (DSLs) have the potential to provide an intuitive interface for specifying problems and solutions for domain experts. Based on this, code generation frameworks can produce compilable source code. However, apart from optimizing execution performance, parallelization is key for pushing the limits in problem size and an essential ingredient for exascale performance. We discuss necessary concepts for the introduction of such capabilities in code generators. In particular, those for partitioning the problem to be solved and accessing the partitioned data are elaborated. Furthermore, possible approaches to expose parallelism to users through a given DSL are discussed. Moreover, we present the implementation of these concepts in the ExaStencils framework. In its scope, a code generation framework for highly optimized and massively parallel geometric multigrid solvers is developed. It uses specifications from its multi-layered external DSL ExaSlang as input. Based on a general version for generating parallel code, we develop and implement widely applicable extensions and optimizations. Finally, a performance study of generated applications is conducted on the JuQueen supercomputer.
      PubDate: 2016-08-04
      DOI: 10.3390/computation4030027
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 28: Highly Excited States from a Time
           Independent Density Functional Method

    • Authors: Vitaly Glushkov, Mel Levy
      First page: 28
      Abstract: A constrained optimized effective potential (COEP) methodology proposed earlier by us for singly low-lying excited states is extended to highly excited states having the same spatial and spin symmetry. Basic tenets of time independent density functional theory and its COEP implementation for excited states are briefly reviewed. The amended Kohn–Sham-like equations for excited state orbitals and their specific features for highly excited states are discussed. The accuracy of the method is demonstrated using exchange-only calculations for highly excited states of the He and Li atoms.
      PubDate: 2016-08-05
      DOI: 10.3390/computation4030028
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 29: DiamondTorre Algorithm for High-Performance
           Wave Modeling

    • Authors: Vadim Levchenko, Anastasia Perepelkina, Andrey Zakirov
      First page: 29
      Abstract: Effective algorithms of physical media numerical modeling problems’ solution are discussed. The computation rate of such problems is limited by memory bandwidth if implemented with traditional algorithms. The numerical solution of the wave equation is considered. A finite difference scheme with a cross stencil and a high order of approximation is used. The DiamondTorre algorithm is constructed, with regard to the specifics of the GPGPU’s (general purpose graphical processing unit) memory hierarchy and parallelism. The advantages of these algorithms are a high level of data localization, as well as the property of asynchrony, which allows one to effectively utilize all levels of GPGPU parallelism. The computational intensity of the algorithm is greater than the one for the best traditional algorithms with stepwise synchronization. As a consequence, it becomes possible to overcome the above-mentioned limitation. The algorithm is implemented with CUDA. For the scheme with the second order of approximation, the calculation performance of 50 billion cells per second is achieved. This exceeds the result of the best traditional algorithm by a factor of five.
      PubDate: 2016-08-12
      DOI: 10.3390/computation4030029
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 30: Electron Correlations in Local Effective
           Potential Theory

    • Authors: Viraht Sahni, Xiao-Yin Pan, Tao Yang
      First page: 30
      Abstract: Local effective potential theory, both stationary-state and time-dependent, constitutes the mapping from a system of electrons in an external field to one of the noninteracting fermions possessing the same basic variable such as the density, thereby enabling the determination of the energy and other properties of the electronic system. This paper is a description via Quantal Density Functional Theory (QDFT) of the electron correlations that must be accounted for in such a mapping. It is proved through QDFT that independent of the form of external field, (a) it is possible to map to a model system possessing all the basic variables; and that (b) with the requirement that the model fermions are subject to the same external fields, the only correlations that must be considered are those due to the Pauli exclusion principle, Coulomb repulsion, and Correlation–Kinetic effects. The cases of both a static and time-dependent electromagnetic field, for which the basic variables are the density and physical current density, are considered. The examples of solely an external electrostatic or time-dependent electric field constitute special cases. An efficacious unification in terms of electron correlations, independent of the type of external field, is thereby achieved. The mapping is explicated for the example of a quantum dot in a magnetostatic field, and for a quantum dot in a magnetostatic and time-dependent electric field.
      PubDate: 2016-08-16
      DOI: 10.3390/computation4030030
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 31: Computational Analysis of Natural
           Ventilation Flows in Geodesic Dome Building in Hot Climates

    • Authors: Zohreh Soleimani, John Calautit, Ben Hughes
      First page: 31
      Abstract: For centuries, dome roofs were used in traditional houses in hot regions such as the Middle East and Mediterranean basin due to its thermal advantages, structural benefits and availability of construction materials. This article presents the computational modelling of the wind- and buoyancy-induced ventilation in a geodesic dome building in a hot climate. The airflow and temperature distributions and ventilation flow rates were predicted using Computational Fluid Dynamics (CFD). The three-dimensional Reynolds-Averaged Navier-Stokes (RANS) equations were solved using the CFD tool ANSYS FLUENT15. The standard k-epsilon was used as turbulence model. The modelling was verified using grid sensitivity and flux balance analysis. In order to validate the modelling method used in the current study, additional simulation of a similar domed-roof building was conducted for comparison. For wind-induced ventilation, the dome building was modelled with upper roof vents. For buoyancy-induced ventilation, the geometry was modelled with roof vents and also with two windows open in the lower level. The results showed that using the upper roof openings as a natural ventilation strategy during winter periods is advantageous and could reduce the indoor temperature and also introduce fresh air. The results also revealed that natural ventilation using roof vents cannot satisfy thermal requirements during hot summer periods and complementary cooling solutions should be considered. The analysis showed that buoyancy-induced ventilation model can still generate air movement inside the building during periods with no or very low wind.
      PubDate: 2016-08-17
      DOI: 10.3390/computation4030031
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 32: Calculation of the Acoustic Spectrum of a
           Cylindrical Vortex in Viscous Heat-Conducting Gas Based on the
           Navier–Stokes Equations

    • Authors: Tatiana Petrova, Fedor Shugaev
      First page: 32
      Abstract: An extremely interesting problem in aero-hydrodynamics is the sound radiation of a single vortical structure. Currently, this type of problem is mainly considered for an incompressible medium. In this paper a method was developed to take into account the viscosity and thermal conductivity of gas. The acoustic radiation frequency of a cylindrical vortex on a flat wall in viscous heat-conducting gas (air) has been investigated. The problem is solved on the basis of the Navier–Stokes equations using the small initial vorticity approach. The power expansion of unknown functions in a series with a small parameter (vorticity) is used. It is shown that there are high-frequency oscillations modulated by a low-frequency signal. The value of the high frequency remains constant for a long period of time. Thus the high frequency can be considered a natural frequency of the vortex radiation. The value of the natural frequency depends only on the initial radius of the cylindrical vortex, and does not depend on the intensity of the initial vorticity. As expected from physical considerations, the natural frequency decreases exponentially as the initial radius of the cylinder increases. Furthermore, the natural frequency differs from that of the oscillations inside the initial cylinder and in the outer domain. The results of the paper may be of interest for aeroacoustics and tornado modeling.
      PubDate: 2016-08-20
      DOI: 10.3390/computation4030032
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 33: The Influence of One-Electron
           Self-Interaction on d-Electrons

    • Authors: Tobias Schmidt, Stephan Kümmel
      First page: 33
      Abstract: We investigate four diatomic molecules containing transition metals using two variants of hybrid functionals. We compare global hybrid functionals that only partially counteract self-interaction to local hybrid functionals that are designed to be formally free from one-electron self-interaction. As d-orbitals are prone to be particularly strongly influenced by self-interaction errors, one may have expected that self-interaction-free local hybrid functionals lead to a qualitatively different Kohn–Sham density of states than global hybrid functionals. Yet, we find that both types of hybrids lead to a very similar density of states. For both global and local hybrids alike, the intrinsic amount of exact exchange plays the dominant role in counteracting electronic self-interaction, whereas being formally free from one-electron self-interaction seems to be of lesser importance.
      PubDate: 2016-09-06
      DOI: 10.3390/computation4030033
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 34: Towards TDDFT for Strongly Correlated
           Materials

    • Authors: Shree Acharya, Volodymyr Turkowski, Talat Rahman
      First page: 34
      Abstract: We present some details of our recently-proposed Time-Dependent Density-Functional Theory (TDDFT) for strongly-correlated materials in which the exchange-correlation (XC) kernel is derived from the charge susceptibility obtained using Dynamical Mean-Field Theory (the TDDFT + DMFT approach). We proceed with deriving the expression for the XC kernel for the one-band Hubbard model by solving DMFT equations via two approaches, the Hirsch–Fye Quantum Monte Carlo (HF-QMC) and an approximate low-cost perturbation theory approach, and demonstrate that the latter gives results that are comparable to the exact HF-QMC solution. Furthermore, through a variety of applications, we propose a simple analytical formula for the XC kernel. Additionally, we use the exact and approximate kernels to examine the nonhomogeneous ultrafast response of two systems: a one-band Hubbard model and a Mott insulator YTiO3. We show that the frequency dependence of the kernel, i.e., memory effects, is important for dynamics at the femtosecond timescale. We also conclude that strong correlations lead to the presence of beats in the time-dependent electric conductivity in YTiO3, a feature that could be tested experimentally and that could help validate the few approximations used in our formulation. We conclude by proposing an algorithm for the generalization of the theory to non-linear response.
      PubDate: 2016-09-10
      DOI: 10.3390/computation4030034
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 35: Image Segmentation for Cardiovascular
           Biomedical Applications at Different Scales

    • Authors: Alexander Danilov, Roman Pryamonosov, Alexandra Yurova
      First page: 35
      Abstract: In this study, we present several image segmentation techniques for various image scales and modalities. We consider cellular-, organ-, and whole organism-levels of biological structures in cardiovascular applications. Several automatic segmentation techniques are presented and discussed in this work. The overall pipeline for reconstruction of biological structures consists of the following steps: image pre-processing, feature detection, initial mask generation, mask processing, and segmentation post-processing. Several examples of image segmentation are presented, including patient-specific abdominal tissues segmentation, vascular network identification and myocyte lipid droplet micro-structure reconstruction.
      PubDate: 2016-09-15
      DOI: 10.3390/computation4030035
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 36: An Extremely Efficient Boundary Element
           Method for Wave Interaction with Long Cylindrical Structures Based on
           Free-Surface Green’s Function

    • Authors: Yingyi Liu, Ying Gou, Bin Teng, Shigeo Yoshida
      First page: 36
      Abstract: The present study aims to develop an efficient numerical method for computing the diffraction and radiation of water waves with horizontal long cylindrical structures, such as floating breakwaters in the coastal region, etc. A higher-order scheme is used to discretize geometry of the structure as well as the physical wave potentials. As the kernel of this method, Wehausen’s free-surface Green function is calculated by a newly-developed Gauss–Kronrod adaptive quadrature algorithm after elimination of its Cauchy-type singularities. To improve its computation efficiency, an analytical solution is derived for a fast evaluation of the Green function that needs to be implemented thousands of times. In addition, the OpenMP parallelization technique is applied to the formation of the influence coefficient matrix, significantly reducing the running CPU time. Computations are performed on wave-exciting forces and hydrodynamic coefficients for the long cylindrical structures, either floating or submerged. Comparison with other numerical and analytical methods demonstrates a good performance of the present method.
      PubDate: 2016-09-16
      DOI: 10.3390/computation4030036
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 37: Computational Streetscapes

    • Authors: Paul Torrens
      First page: 37
      Abstract: Streetscapes have presented a long-standing interest in many fields. Recently, there has been a resurgence of attention on streetscape issues, catalyzed in large part by computing. Because of computing, there is more understanding, vistas, data, and analysis of and on streetscape phenomena than ever before. This diversity of lenses trained on streetscapes permits us to address long-standing questions, such as how people use information while mobile, how interactions with people and things occur on streets, how we might safeguard crowds, how we can design services to assist pedestrians, and how we could better support special populations as they traverse cities. Amid each of these avenues of inquiry, computing is facilitating new ways of posing these questions, particularly by expanding the scope of what-if exploration that is possible. With assistance from computing, consideration of streetscapes now reaches across scales, from the neurological interactions that form among place cells in the brain up to informatics that afford real-time views of activity over whole urban spaces. For some streetscape phenomena, computing allows us to build realistic but synthetic facsimiles in computation, which can function as artificial laboratories for testing ideas. In this paper, I review the domain science for studying streetscapes from vantages in physics, urban studies, animation and the visual arts, psychology, biology, and behavioral geography. I also review the computational developments shaping streetscape science, with particular emphasis on modeling and simulation as informed by data acquisition and generation, data models, path-planning heuristics, artificial intelligence for navigation and way-finding, timing, synthetic vision, steering routines, kinematics, and geometrical treatment of collision detection and avoidance. I also discuss the implications that the advances in computing streetscapes might have on emerging developments in cyber-physical systems and new developments in urban computing and mobile computing.
      PubDate: 2016-09-20
      DOI: 10.3390/computation4030037
      Issue No: Vol. 4, No. 3 (2016)
       
  • Computation, Vol. 4, Pages 16: Current Issues in Finite-T
           Density-Functional Theory and Warm-Correlated Matter †

    • Authors: M. Dharma-wardana
      First page: 16
      Abstract: Finite-temperature density functional theory (DFT) has become of topical interest, partly due to the increasing ability to create novel states of warm-correlated matter (WCM). Warm-dense matter (WDM), ultra-fast matter (UFM), and high-energy density matter (HEDM) may all be regarded as subclasses of WCM. Strong electron-electron, ion-ion and electron-ion correlation effects and partial degeneracies are found in these systems where the electron temperature T e is comparable to the electron Fermi energy E F . Thus, many electrons are in continuum states which are partially occupied. The ion subsystem may be solid, liquid or plasma, with many states of ionization with ionic charge Z j . Quasi-equilibria with the ion temperature T i ≠ T e are common. The ion subsystem in WCM can no longer be treated as a passive “external potential”, as is customary in T = 0 DFT dominated by solid-state theory or quantum chemistry. Many basic questions arise in trying to implement DFT for WCM. Hohenberg-Kohn-Mermin theory can be adapted for treating these systems if suitable finite-T exchange-correlation (XC) functionals can be constructed. They are functionals of both the one-body electron density n e and the one-body ion densities ρ j . Here, j counts many species of nuclei or charge states. A method of approximately but accurately mapping the quantum electrons to a classical Coulomb gas enables one to treat electron-ion systems entirely classically at any temperature and arbitrary spin polarization, using exchange-correlation effects calculated in situ, directly from the pair-distribution functions. This eliminates the need for any XC-functionals. This classical map has been used to calculate the equation of state of WDM systems, and construct a finite-T XC functional that is found to be in close agreement with recent quantum path-integral simulation data. In this review, current developments and concerns in finite-T DFT, especially in the context of non-relativistic warm-dense matter and ultra-fast matter will be presented.
      PubDate: 2016-03-28
      DOI: 10.3390/computation4020016
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 17: Analytical Results on the Behavior of a
           Liquid Junction across a Porous Diaphragm or a Charged Porous Membrane
           between Two Solutions According to the Nernst–Planck Equation

    • Authors: Massimo Marino, Doriano Brogioli
      First page: 17
      Abstract: We model the behavior of an ideal liquid junction, across a porous and possibly charged medium between two ion-containing solutions, by means of the Nernst–Planck equation for the stationary state, in conditions of local electroneutrality. An analytical solution of the equation was found long ago by Planck for the uncharged junction with only ions of valences +1 and −1. Other analytical results, which have later been obtained also for more general situations, seem impractical for performing calculations. In this paper, we obtain analytical solutions for systems with up to three valence classes, which can be applied to perform numerical calculations in a straightforward way. Our method provides a much larger amount of information on the behavior of the system than the well-known Henderson’s approximation. At the same time, it is more simple and reliable, and much less demanding in terms of computational effort, than the nowadays commonly employed numerical methods, typically based on discrete integration and trial-and-error numerical inversions. We present some examples of practical applications of our results. We study in particular the uphill transport (i.e., the transport from the lower-concentration to the higher-concentration region) of a divalent cation in a liquid junction containing also other univalent anions and cations.
      PubDate: 2016-03-30
      DOI: 10.3390/computation4020017
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 18: Grand Canonical Monte Carlo Simulation of
           Nitrogen Adsorption in a Silica Aerogel Model

    • Authors: Wen-Li Xie, Zheng-Ji Chen, Zeng Li, Wen-Quan Tao
      First page: 18
      Abstract: In this paper, the Diffusion Limited Cluster Aggregation (DLCA) method is employed to reconstruct the three-dimensional network of silica aerogel. Then, simulation of nitrogen adsorption at 77 K in silica aerogel is conducted by the Grand Canonical Monte Carlo (GCMC) method. To reduce the computational cost and guarantee accuracy, a continuous-discrete hybrid potential model, as well as an adsorbed layer thickness estimation method, is employed. Four different structures are generated to investigate impacts of specific surface area and porosity on adsorptive capacity. Good agreement with experimental results is found over a wide range of relative pressures, which proves the validity of the model. Specific surface area and porosity mainly affect nitrogen uptake under low pressure and high pressure, respectively.
      PubDate: 2016-04-01
      DOI: 10.3390/computation4020018
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 19: Kinetic and Exchange Energy Densities near
           the Nucleus

    • Authors: Lucian Constantin, Eduardo Fabiano, Fabio Della Sala
      First page: 19
      Abstract: We investigate the behavior of the kinetic and the exchange energy densities near the nuclear cusp of atomic systems. Considering hydrogenic orbitals, we derive analytical expressions near the nucleus, for single shells, as well as in the semiclassical limit of large non-relativistic neutral atoms. We show that a model based on the helium iso-electronic series is very accurate, as also confirmed by numerical calculations on real atoms up to two thousands electrons. Based on this model, we propose non-local density-dependent ingredients that are suitable for the description of the kinetic and exchange energy densities in the region close to the nucleus. These non-local ingredients are invariant under the uniform scaling of the density, and they can be used in the construction of non-local exchange-correlation and kinetic functionals.
      PubDate: 2016-04-02
      DOI: 10.3390/computation4020019
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 20: On the Use of Benchmarks for Multiple
           Properties

    • Authors: Bartolomeo Civalleri, Roberto Dovesi, Pascal Pernot, Davide Presti, Andreas Savin
      First page: 20
      Abstract: Benchmark calculations provide a large amount of information that can be very useful in assessing the performance of density functional approximations, and for choosing the one to use. In order to condense the information some indicators are provided. However, these indicators might be insufficient and a more careful analysis is needed, as shown by some examples from an existing data set for cubic crystals.
      PubDate: 2016-04-30
      DOI: 10.3390/computation4020020
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 21: Pore-Network Modeling of Water and Vapor
           Transport in the Micro Porous Layer and Gas Diffusion Layer of a Polymer
           Electrolyte Fuel Cell

    • Authors: Chao-Zhong Qin, S. Hassanizadeh, Lucas Van Oosterhout
      First page: 21
      Abstract: In the cathode side of a polymer electrolyte fuel cell (PEFC), a micro porous layer (MPL) added between the catalyst layer (CL) and the gas diffusion layer (GDL) plays an important role in water management. In this work, by using both quasi-static and dynamic pore-network models, water and vapor transport in the MPL and GDL has been investigated. We illustrated how the MPL improved water management in the cathode. Furthermore, it was found that dynamic liquid water transport in the GDL was very sensitive to the built-up thermal gradient along the through-plane direction. Thus, we may control water vapor condensation only along GDL-land interfaces by properly adjusting the GDL thermal conductivity. Our numerical results can provide guidelines for optimizing GDL pore structures for good water management.
      PubDate: 2016-05-30
      DOI: 10.3390/computation4020021
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 22: Online Adaptive Local-Global Model
           Reduction for Flows in Heterogeneous Porous Media

    • Authors: Yalchin Efendiev, Eduardo Gildin, Yanfang Yang
      First page: 22
      Abstract: We propose an online adaptive local-global POD-DEIM model reduction method for flows in heterogeneous porous media. The main idea of the proposed method is to use local online indicators to decide on the global update, which is performed via reduced cost local multiscale basis functions. This unique local-global online combination allows (1) developing local indicators that are used for both local and global updates (2) computing global online modes via local multiscale basis functions. The multiscale basis functions consist of offline and some online local basis functions. The approach used for constructing a global reduced system is based on Proper Orthogonal Decomposition (POD) Galerkin projection. The nonlinearities are approximated by the Discrete Empirical Interpolation Method (DEIM). The online adaption is performed by incorporating new data, which become available at the online stage. Once the criterion for updates is satisfied, we adapt the reduced system online by changing the POD subspace and the DEIM approximation of the nonlinear functions. The main contribution of the paper is that the criterion for adaption and the construction of the global online modes are based on local error indicators and local multiscale basis function which can be cheaply computed. Since the adaption is performed infrequently, the new methodology does not add significant computational overhead associated with when and how to adapt the reduced basis. Our approach is particularly useful for situations where it is desired to solve the reduced system for inputs or controls that result in a solution outside the span of the snapshots generated in the offline stage. Our method also offers an alternative of constructing a robust reduced system even if a potential initial poor choice of snapshots is used. Applications to single-phase and two-phase flow problems demonstrate the efficiency of our method.
      PubDate: 2016-06-07
      DOI: 10.3390/computation4020022
      Issue No: Vol. 4, No. 2 (2016)
       
  • Computation, Vol. 4, Pages 3: A Test of Various Partial Atomic Charge
           Models for Computations on Diheteroaryl Ketones and Thioketones

    • Authors: Piotr Matczak
      First page: 3
      Abstract: The effective use of partial atomic charge models is essential for such purposes in molecular computations as a simplified representation of global charge distribution in a molecule and predicting its conformational behavior. In this work, ten of the most popular models of partial atomic charge are taken into consideration, and these models operate on the molecular wave functions/electron densities of five diheteroaryl ketones and their thiocarbonyl analogs. The ten models are tested in order to assess their usefulness in achieving the aforementioned purposes for the compounds in title. Therefore, the following criteria are used in the test: (1) how accurately these models reproduce the molecular dipole moments of the conformers of the investigated compounds; (2) whether these models are able to correctly determine the preferred conformer as well as the ordering of higher-energy conformers for each compound. The results of the test indicate that the Merz-Kollman-Singh (MKS) and Hu-Lu-Yang (HLY) models approximate the magnitude of the molecular dipole moments with the greatest accuracy. The natural partial atomic charges perform best in determining the conformational behavior of the investigated compounds. These findings may constitute important support for the effective computations of electrostatic effects occurring within and between the molecules of the compounds in question as well as similar compounds.
      PubDate: 2016-01-19
      DOI: 10.3390/computation4010003
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 4: Acknowledgement to Reviewers of Computation
           in 2015

    • Authors: Computation Editorial Office
      First page: 4
      Abstract: The editors of Computation would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...]
      PubDate: 2016-01-22
      DOI: 10.3390/computation4010004
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 5: Extracting Conformational Ensembles of Small
           Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

    • Authors: Giuliano Malloci, Giovanni Serra, Andrea Bosin, Attilio Vargiu
      First page: 5
      Abstract: The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD) trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD) and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different charge/protonation states of ampicillin, we made available force-field parameters and static/dynamic properties derived from both Density Functional Theory and MD calculations. For the specific system investigated here, we found that: (i) the conformational statistics extracted from plain MD simulations is consistent with that obtained from REMD simulations; (ii) overall, our MD-based approach performs slightly better than any of the conformer generator tools if one takes into account both the diversity of the generated conformational set and the ability to reproduce experimentally-determined structures.
      PubDate: 2016-01-26
      DOI: 10.3390/computation4010005
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 6: Computation of the Likelihood of Joint Site
           Frequency Spectra Using Orthogonal Polynomials

    • Authors: Claus Vogl, Juraj Bergman
      First page: 6
      Abstract: In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, DNA consists of two long strands of nucleotides or sites that pair via the complementary bases cytosine and guanine (C and G), on the one hand, and adenine and thymine (A and T), on the other. With whole genome sequencing, most genomic information stored in the DNA has become available for multiple individuals of one or more populations, at least in humans and model species, such as fruit flies of the genus Drosophila. In a genome-wide sample of L sites for M (haploid) individuals, the state of each site may be made binary, by binning the complementary bases, e.g., C with G to C/G, and contrasting C/G to A/T, to obtain a “site frequency spectrum” (SFS). Two such samples of either a single population from different time-points or two related populations from a single time-point are called joint site frequency spectra (joint SFS). While mathematical models describing the interplay of mutation, drift and selection have been available for more than 80 years, calculation of exact likelihoods from joint SFS is difficult. Sufficient statistics for inference of, e.g., mutation or selection parameters that would make use of all the information in the genomic data are rarely available. Hence, often suites of crude summary statistics are combined in simulation-based computational approaches. In this article, we use a bi-allelic boundary-mutation and drift population genetic model to compute the transition probabilities of joint SFS using orthogonal polynomials. This allows inference of population genetic parameters, such as the mutation rate (scaled by the population size) and the time separating the two samples. We apply this inference method to a population dataset of neutrally-evolving short intronic sites from six DNA sequences of the fruit fly Drosophila melanogaster and the reference sequence of the related species Drosophila sechellia.
      PubDate: 2016-02-04
      DOI: 10.3390/computation4010006
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 7: Applications of Computational Modelling and
           Simulation of Porous Medium in Tissue Engineering

    • Authors: Carrie German, Sundararajan Madihally
      First page: 7
      Abstract: In tissue engineering, porous biodegradable scaffolds are used as templates for regenerating required tissues. With the advances in computational tools, many modeling approaches have been considered. For example, fluid flow through porous medium can be modeled using the Brinkman equation where permeability of the porous medium has to be defined. In this review, we summarize various models recently reported for defining permeability and non-invasive pressure drop monitoring as a tool to validate dynamic changes in permeability. We also summarize some models used for scaffold degradation and integrating mass transport in the simulation.
      PubDate: 2016-02-06
      DOI: 10.3390/computation4010007
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 8: CFD Simulation and Experimental Analyses of
           a Copper Wire Woven Heat Exchanger Design to Improve Heat Transfer and
           Reduce the Size of Adsorption Beds

    • Authors: John White
      First page: 8
      Abstract: The chief objective of this study is the proposal design and CFD simulation of a new compacted copper wire woven fin heat exchanger and silica gel adsorbent bed used as part of an adsorption refrigeration system. This type of heat exchanger design has a large surface area because of the wire woven fin design. It is estimated that this will help improve the coefficient of performance (COP) of the adsorption phase and increase the heat transfer in this system arrangement. To study the heat transfer between the fins and porous adsorbent reactor bed, two experiments were carried out and matched to computational fluid dynamics (CFD) results.
      PubDate: 2016-02-06
      DOI: 10.3390/computation4010008
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 9: A New Method to Infer Advancement of Saline
           Front in Coastal Groundwater Systems by 3D: The Case of Bari (Southern
           Italy) Fractured Aquifer

    • Authors: Costantino Masciopinto, Domenico Palmiotta
      First page: 9
      Abstract: A new method to study 3D saline front advancement in coastal fractured aquifers has been presented. Field groundwater salinity was measured in boreholes of the Bari (Southern Italy) coastal aquifer with depth below water table. Then, the Ghyben-Herzberg freshwater/saltwater (50%) sharp interface and saline front position were determined by model simulations of the freshwater flow in groundwater. Afterward, the best-fit procedure between groundwater salinity measurements, at assigned water depth of 1.0 m in boreholes, and distances of each borehole from the modelled freshwater/saltwater saline front was used to convert each position (x, y) in groundwater to the water salinity concentration at depth of 1.0 m. Moreover, a second best-fit procedure was applied to the salinity measurements in boreholes with depth z. These results provided a grid file (x, y, z, salinity) suitable for plotting the actual Bari aquifer salinity by 3D maps. Subsequently, in order to assess effects of pumping on the saltwater-freshwater transition zone in the coastal aquifer, the Navier-Stokes (N-S) equations were applied to study transient density-driven flow and salt mass transport into freshwater of a single fracture. The rate of seawater/freshwater interface advancement given by the N-S solution was used to define the progression of saline front in Bari groundwater, starting from the actual salinity 3D map. The impact of pumping of 335 L·s−1 during the transition period of 112.8 days was easily highlighted on 3D salinity maps of Bari aquifer.
      PubDate: 2016-02-16
      DOI: 10.3390/computation4010009
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 10: Localized Polycentric Orbital Basis Set for
           Quantum Monte Carlo Calculations Derived from the Decomposition of
           Kohn-Sham Optimized Orbitals

    • Authors: Claudio Amovilli, Franca Floris, Andrea Grisafi
      First page: 10
      Abstract: In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT) calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy.
      PubDate: 2016-02-06
      DOI: 10.3390/computation4010010
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 11: Enhancing Computational Precision for
           Lattice Boltzmann Schemes in Porous Media Flows

    • Authors: Farrel Gray, Edo Boek
      First page: 11
      Abstract: We reassess a method for increasing the computational accuracy of lattice Boltzmann schemes by a simple transformation of the distribution function originally proposed by Skordos which was found to give a marginal increase in accuracy in the original paper. We restate the method and give further important implementation considerations which were missed in the original work and show that this method can in fact enhance the precision of velocity field calculations by orders of magnitude and does not lose accuracy when velocities are small, unlike the usual LB approach. The analysis is framed within the multiple-relaxation-time method for porous media flows, however the approach extends directly to other lattice Boltzmann schemes. First, we compute the flow between parallel plates and compare the error from the analytical profile for the traditional approach and the transformed scheme using single (4-byte) and double (8-byte) precision. Then we compute the flow inside a complex-structured porous medium and show that the traditional approach using single precision leads to large, systematic errors compared to double precision, whereas the transformed approach avoids this issue whilst maintaining all the computational efficiency benefits of using single precision.
      PubDate: 2016-02-17
      DOI: 10.3390/computation4010011
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 12: Contact Angle Effects on Pore and Corner
           Arc Menisci in Polygonal Capillary Tubes Studied with the Pseudopotential
           Multiphase Lattice Boltzmann Model

    • Authors: Soyoun Son, Li Chen, Qinjun Kang, Dominique Derome, Jan Carmeliet
      First page: 12
      Abstract: In porous media, pore geometry and wettability are determinant factors for capillary flow in drainage or imbibition. Pores are often considered as cylindrical tubes in analytical or computational studies. Such simplification prevents the capture of phenomena occurring in pore corners. Considering the corners of pores is crucial to realistically study capillary flow and to accurately estimate liquid distribution, degree of saturation and dynamic liquid behavior in pores and in porous media. In this study, capillary flow in polygonal tubes is studied with the Shan-Chen pseudopotential multiphase lattice Boltzmann model (LBM). The LB model is first validated through a contact angle test and a capillary intrusion test. Then capillary rise in square and triangular tubes is simulated and the pore meniscus height is investigated as a function of contact angle θ. Also, the occurrence of fluid in the tube corners, referred to as corner arc menisci, is studied in terms of curvature versus degree of saturation. In polygonal capillary tubes, the number of sides leads to a critical contact angle θc which is known as a key parameter for the existence of the two configurations. LBM succeeds in simulating the formation of a pore meniscus at θ > θc or the occurrence of corner arc menisci at θ < θc. The curvature of corner arc menisci is known to decrease with increasing saturation and decreasing contact angle as described by the Mayer and Stoewe-Princen (MS-P) theory. We obtain simulation results that are in good qualitative and quantitative agreement with the analytical solutions in terms of height of pore meniscus versus contact angle and curvature of corner arc menisci versus saturation degree. LBM is a suitable and promising tool for a better understanding of the complicated phenomena of multiphase flow in porous media.
      PubDate: 2016-02-20
      DOI: 10.3390/computation4010012
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 13: Direct Numerical Simulation of Turbulent
           Channel Flow on High-Performance GPU Computing System

    • Authors: Giancarlo Alfonsi, Stefania Ciliberti, Marco Mancini, Leonardo Primavera
      First page: 13
      Abstract: The flow of a viscous fluid in a plane channel is simulated numerically following the DNS approach, and using a computational code for the numerical integration of the Navier-Stokes equations implemented on a hybrid CPU/GPU computing architecture (for the meaning of symbols and acronyms used, one can refer to the Nomenclature). Three turbulent-flow databases, each representing the turbulent statistically-steady state of the flow at three different values of the Reynolds number, are built up, and a number of statistical moments of the fluctuating velocity field are computed. For turbulent-flow-structure investigation, the vortex-detection technique of the imaginary part of the complex eigenvalue pair in the velocity-gradient tensor is applied to the fluctuating-velocity fields. As a result, and among other types, hairpin vortical structures are unveiled. The processes of evolution that characterize the hairpin vortices in the near-wall region of the turbulent channel are investigated, in particular at one of the three Reynolds numbers tested, with specific attention given to the relationship that exists between the dynamics of the vortical structures and the occurrence of ejection and sweep quadrant events. Interestingly, it is found that the latter events play a preminent role in the way in which the morphological evolution of a hairpin vortex develops over time, as related in particular to the establishment of symmetric and persistent hairpins. The present results have been obtained from a database that incorporates genuine DNS solutions of the Navier-Stokes equations, without superposition of any synthetic structures in the form of initial and/or boundary conditions for the simulations.
      PubDate: 2016-02-26
      DOI: 10.3390/computation4010013
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 14: Influence of the Localization of Ge Atoms
           within the Si(001)(4 × 2) Surface Layer on Semicore One-Electron States

    • Authors: Olha Tkachuk, Maria Terebinskaya, Victor Lobanov, Alexei Arbuznikov
      First page: 14
      Abstract: Adsorption complexes of germanium on the reconstructed Si(001)(4 × 2) surface have been simulated by the Si96Ge2Н84 cluster. For Ge atoms located on the surface layer, DFT calculations (B3LYP/6-31G**) of their 3d semicore-level energies have shown a clear-cut correlation between the 3d5/2 chemical shifts and mutual arrangement of Ge atoms. Such a shift is positive when only one Ge atom penetrates into the crystalline substrate, while being negative for both penetrating Ge atoms. We interpret these results in terms of the charge distribution in clusters under consideration.
      PubDate: 2016-03-03
      DOI: 10.3390/computation4010014
      Issue No: Vol. 4, No. 1 (2016)
       
  • Computation, Vol. 4, Pages 15: Bonding Strength Effects in
           Hydro-Mechanical Coupling Transport in Granular Porous Media by Pore-Scale
           Modeling

    • Authors: Zhiqiang Chen, Chiyu Xie, Yu Chen, Moran Wang
      First page: 15
      Abstract: The hydro-mechanical coupling transport process of sand production is numerically investigated with special attention paid to the bonding effect between sand grains. By coupling the lattice Boltzmann method (LBM) and the discrete element method (DEM), we are able to capture particles movements and fluid flows simultaneously. In order to account for the bonding effects on sand production, a contact bond model is introduced into the LBM-DEM framework. Our simulations first examine the experimental observation of “initial sand production is evoked by localized failure” and then show that the bonding or cement plays an important role in sand production. Lower bonding strength will lead to more sand production than higher bonding strength. It is also found that the influence of flow rate on sand production depends on the bonding strength in cemented granular media, and for low bonding strength sample, the higher the flow rate is, the more severe the erosion found in localized failure zone becomes.
      PubDate: 2016-03-07
      DOI: 10.3390/computation4010015
      Issue No: Vol. 4, No. 1 (2016)
       
 
 
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