Computation
http://www.mdpi.com/journal/computation
Latest open access articles published in Computation at http://www.mdpi.com/journal/computation<![CDATA[Computation, Vol. 5, Pages 19: Esoteric Twist: An Efficient in-Place Streaming Algorithmus for the Lattice Boltzmann Method on Massively Parallel Hardware]]>
http://www.mdpi.com/2079-3197/5/2/19
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.Computation2017-03-2352Article10.3390/computation5020019192079-31972017-03-23doi: 10.3390/computation5020019Martin GeierMartin Schönherr<![CDATA[Computation, Vol. 5, Pages 18: An Accurate Computational Tool for Performance Estimation of FSO Communication Links over Weak to Strong Atmospheric Turbulent Channels]]>
http://www.mdpi.com/2079-3197/5/1/18
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.Computation2017-03-1851Article10.3390/computation5010018182079-31972017-03-18doi: 10.3390/computation5010018Theodore D. KatsilierisGeorge P. LatsasHector E. NistazakisGeorge S. Tombras<![CDATA[Computation, Vol. 5, Pages 17: Evaluation of Soil-Structure Interaction on the Seismic Response of Liquid Storage Tanks under Earthquake Ground Motions]]>
http://www.mdpi.com/2079-3197/5/1/17
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.Computation2017-03-1251Article10.3390/computation5010017172079-31972017-03-12doi: 10.3390/computation5010017Mostafa FarajianMohammad KhodakaramiDenise-Penelope Kontoni<![CDATA[Computation, Vol. 5, Pages 16: A Hybrid Computation Model to Describe the Progression of Multiple Myeloma and Its Intra-Clonal Heterogeneity]]>
http://www.mdpi.com/2079-3197/5/1/16
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.Computation2017-03-1051Article10.3390/computation5010016162079-31972017-03-10doi: 10.3390/computation5010016Anass BouchnitaFatima-Ezzahra BelmaatiRajae AboulaichMark KouryVitaly Volpert<![CDATA[Computation, Vol. 5, Pages 14: Simpliﬁcation of Reaction Networks, Conﬂuence and Elementary Modes]]>
http://www.mdpi.com/2079-3197/5/1/14
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.Computation2017-03-1051Article10.3390/computation5010014142079-31972017-03-10doi: 10.3390/computation5010014Guillaume MadelaineElisa TonelloCédric LhoussaineJoachim Niehren<![CDATA[Computation, Vol. 5, Pages 15: Schrödinger Theory of Electrons in Electromagnetic Fields: New Perspectives]]>
http://www.mdpi.com/2079-3197/5/1/15
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.Computation2017-03-0951Article10.3390/computation5010015152079-31972017-03-09doi: 10.3390/computation5010015Viraht SahniXiao-Yin Pan<![CDATA[Computation, Vol. 5, Pages 13: Aerodynamic Performance of a NREL S809 Airfoil in an Air-Sand Particle Two-Phase Flow]]>
http://www.mdpi.com/2079-3197/5/1/13
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.Computation2017-02-2851Article10.3390/computation5010013132079-31972017-02-28doi: 10.3390/computation5010013Dimitra DouviDionissios MargarisAristeidis Davaris<![CDATA[Computation, Vol. 5, Pages 12: Numerical Modelling of Double-Steel Plate Composite Shear Walls]]>
http://www.mdpi.com/2079-3197/5/1/12
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.Computation2017-02-2251Article10.3390/computation5010012122079-31972017-02-22doi: 10.3390/computation5010012Michaela ElmatzoglouAris Avdelas<![CDATA[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]]>
http://www.mdpi.com/2079-3197/5/1/11
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.Computation2017-02-1851Article10.3390/computation5010011112079-31972017-02-18doi: 10.3390/computation5010011Andrey GolovSergey SimakovYan SoeRoman PryamonosovOspan MynbaevAlexander Kholodov<![CDATA[Computation, Vol. 5, Pages 10: Virtual Prototyping and Validation of Cpps within a New Software Framework]]>
http://www.mdpi.com/2079-3197/5/1/10
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.Computation2017-02-1851Article10.3390/computation5010010102079-31972017-02-18doi: 10.3390/computation5010010Sebastian NeumeyerKonrad ExnerSimon KindHaygazun HaykaRainer Stark<![CDATA[Computation, Vol. 5, Pages 9: Excitons in Solids from Time-Dependent Density-Functional Theory: Assessing the Tamm-Dancoff Approximation]]>
http://www.mdpi.com/2079-3197/5/1/9
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.Computation2017-01-2951Article10.3390/computation501000992079-31972017-01-29doi: 10.3390/computation5010009Young-Moo ByunCarsten Ullrich<![CDATA[Computation, Vol. 5, Pages 8: Numerical and Computational Analysis of a New Vertical Axis Wind Turbine, Named KIONAS]]>
http://www.mdpi.com/2079-3197/5/1/8
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.Computation2017-01-1151Article10.3390/computation501000882079-31972017-01-11doi: 10.3390/computation5010008Eleni DouviDimitra DouviDionissios MargarisIoannis Drosis<![CDATA[Computation, Vol. 5, Pages 7: Acknowledgement to Reviewers of Computation in 2016]]>
http://www.mdpi.com/2079-3197/5/1/7
The editors of Computation would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016.[...]Computation2017-01-1051Editorial10.3390/computation501000772079-31972017-01-10doi: 10.3390/computation5010007 Computation Editorial Office<![CDATA[Computation, Vol. 5, Pages 6: Towards a Multiscale Model of Acute HIV Infection]]>
http://www.mdpi.com/2079-3197/5/1/6
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.Computation2017-01-1051Article10.3390/computation501000662079-31972017-01-10doi: 10.3390/computation5010006Anass BouchnitaGennady BocharovAndreas MeyerhansVitaly Volpert<![CDATA[Computation, Vol. 5, Pages 4: An SVM Framework for Malignant Melanoma Detection Based on Optimized HOG Features]]>
http://www.mdpi.com/2079-3197/5/1/4
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.Computation2017-01-0151Article10.3390/computation501000442079-31972017-01-01doi: 10.3390/computation5010004Samy Bakheet<![CDATA[Computation, Vol. 5, Pages 5: First Principle Modelling of Materials and Processes in Dye-Sensitized Photoanodes for Solar Energy and Solar Fuels]]>
http://www.mdpi.com/2079-3197/5/1/5
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.Computation2017-01-0151Review10.3390/computation501000552079-31972017-01-01doi: 10.3390/computation5010005Mariachiara Pastore<![CDATA[Computation, Vol. 5, Pages 3: Critical Issues in Modelling Lymph Node Physiology]]>
http://www.mdpi.com/2079-3197/5/1/3
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.Computation2016-12-2451Article10.3390/computation501000332079-31972016-12-24doi: 10.3390/computation5010003Dmitry GrebennikovRaoul van LoonMario NovkovicLucas OnderRostislav SavinkovIgor SazonovRufina TretyakovaDaniel WatsonGennady Bocharov<![CDATA[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]]>
http://www.mdpi.com/2079-3197/5/1/2
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.Computation2016-12-2351Article10.3390/computation501000222079-31972016-12-23doi: 10.3390/computation5010002Supratik KarJuganta RoyDanuta LeszczynskaJerzy Leszczynski<![CDATA[Computation, Vol. 5, Pages 1: Application of the Recursive Finite Element Approach on 2D Periodic Structures under Harmonic Vibrations]]>
http://www.mdpi.com/2079-3197/5/1/1
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.Computation2016-12-2251Article10.3390/computation501000112079-31972016-12-22doi: 10.3390/computation5010001Reem YassineFaten SalmanAli Al ShaerMohammad HammoudDenis Duhamel<![CDATA[Computation, Vol. 4, Pages 46: Effect of Pore Structure on Soot Deposition in Diesel Particulate Filter]]>
http://www.mdpi.com/2079-3197/4/4/46
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.Computation2016-12-0244Article10.3390/computation4040046462079-31972016-12-02doi: 10.3390/computation4040046Kazuhiro YamamotoTatsuya Sakai<![CDATA[Computation, Vol. 4, Pages 45: Special Issue “50th Anniversary of the Kohn–Sham Theory—Advances in Density Functional Theory”]]>
http://www.mdpi.com/2079-3197/4/4/45
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.Computation2016-11-2244Editorial10.3390/computation4040045452079-31972016-11-22doi: 10.3390/computation4040045Ágnes NagyKarlheinz Schwarz<![CDATA[Computation, Vol. 4, Pages 43: A Theoretical Study of One- and Two-Photon Activity of D-Luciferin]]>
http://www.mdpi.com/2079-3197/4/4/43
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.Computation2016-11-1744Article10.3390/computation4040043432079-31972016-11-17doi: 10.3390/computation4040043Mausumi ChattopadhyayaMd. Alam<![CDATA[Computation, Vol. 4, Pages 44: Mathematical Model of a Lithium-Bromide/Water Absorption Refrigeration System Equipped with an Adiabatic Absorber]]>
http://www.mdpi.com/2079-3197/4/4/44
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.Computation2016-11-1744Article10.3390/computation4040044442079-31972016-11-17doi: 10.3390/computation4040044Salem Osta-OmarChristopher Micallef<![CDATA[Computation, Vol. 4, Pages 42: A Mathematical Spline-Based Model of Cardiac Left Ventricle Anatomy and Morphology]]>
http://www.mdpi.com/2079-3197/4/4/42
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.Computation2016-10-2744Article10.3390/computation4040042422079-31972016-10-27doi: 10.3390/computation4040042Sergei Pravdin<![CDATA[Computation, Vol. 4, Pages 41: Evaluation of External Memory Access Performance on a High-End FPGA Hybrid Computer]]>
http://www.mdpi.com/2079-3197/4/4/41
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.Computation2016-10-2544Article10.3390/computation4040041412079-31972016-10-25doi: 10.3390/computation4040041Konstantinos KalaitzisEvripidis SotiriadisIoannis PapaefstathiouApostolos Dollas<![CDATA[Computation, Vol. 4, Pages 39: A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection]]>
http://www.mdpi.com/2079-3197/4/4/39
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.Computation2016-10-2144Article10.3390/computation4040039392079-31972016-10-21doi: 10.3390/computation4040039Simeone MarinoDenise Kirschner<![CDATA[Computation, Vol. 4, Pages 40: Obituary for Walter Kohn (1923–2016)]]>
http://www.mdpi.com/2079-3197/4/4/40
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. [...]Computation2016-10-2044Editorial10.3390/computation4040040402079-31972016-10-20doi: 10.3390/computation4040040Karlheinz SchwarzLu ShamAnn MattssonMatthias Scheffler<![CDATA[Computation, Vol. 4, Pages 38: Steady-State Anderson Accelerated Coupling of Lattice Boltzmann and Navier–Stokes Solvers]]>
http://www.mdpi.com/2079-3197/4/4/38
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.Computation2016-10-1744Article10.3390/computation4040038382079-31972016-10-17doi: 10.3390/computation4040038Atanas AtanasovBenjamin UekermannCarlos Pachajoa MejíaHans-Joachim BungartzPhilipp Neumann<![CDATA[Computation, Vol. 4, Pages 37: Computational Streetscapes]]>
http://www.mdpi.com/2079-3197/4/3/37
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.Computation2016-09-2043Review10.3390/computation4030037372079-31972016-09-20doi: 10.3390/computation4030037Paul Torrens<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/3/36
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.Computation2016-09-1643Article10.3390/computation4030036362079-31972016-09-16doi: 10.3390/computation4030036Yingyi LiuYing GouBin TengShigeo Yoshida<![CDATA[Computation, Vol. 4, Pages 35: Image Segmentation for Cardiovascular Biomedical Applications at Different Scales]]>
http://www.mdpi.com/2079-3197/4/3/35
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.Computation2016-09-1543Article10.3390/computation4030035352079-31972016-09-15doi: 10.3390/computation4030035Alexander DanilovRoman PryamonosovAlexandra Yurova<![CDATA[Computation, Vol. 4, Pages 34: Towards TDDFT for Strongly Correlated Materials]]>
http://www.mdpi.com/2079-3197/4/3/34
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.Computation2016-09-1043Article10.3390/computation4030034342079-31972016-09-10doi: 10.3390/computation4030034Shree AcharyaVolodymyr TurkowskiTalat Rahman<![CDATA[Computation, Vol. 4, Pages 33: The Influence of One-Electron Self-Interaction on d-Electrons]]>
http://www.mdpi.com/2079-3197/4/3/33
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.Computation2016-09-0643Article10.3390/computation4030033332079-31972016-09-06doi: 10.3390/computation4030033Tobias SchmidtStephan Kümmel<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/3/32
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.Computation2016-08-2043Article10.3390/computation4030032322079-31972016-08-20doi: 10.3390/computation4030032Tatiana PetrovaFedor Shugaev<![CDATA[Computation, Vol. 4, Pages 31: Computational Analysis of Natural Ventilation Flows in Geodesic Dome Building in Hot Climates]]>
http://www.mdpi.com/2079-3197/4/3/31
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.Computation2016-08-1743Article10.3390/computation4030031312079-31972016-08-17doi: 10.3390/computation4030031Zohreh SoleimaniJohn CalautitBen Hughes<![CDATA[Computation, Vol. 4, Pages 30: Electron Correlations in Local Effective Potential Theory]]>
http://www.mdpi.com/2079-3197/4/3/30
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.Computation2016-08-1643Article10.3390/computation4030030302079-31972016-08-16doi: 10.3390/computation4030030Viraht SahniXiao-Yin PanTao Yang<![CDATA[Computation, Vol. 4, Pages 29: DiamondTorre Algorithm for High-Performance Wave Modeling]]>
http://www.mdpi.com/2079-3197/4/3/29
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.Computation2016-08-1243Article10.3390/computation4030029292079-31972016-08-12doi: 10.3390/computation4030029Vadim LevchenkoAnastasia PerepelkinaAndrey Zakirov<![CDATA[Computation, Vol. 4, Pages 28: Highly Excited States from a Time Independent Density Functional Method]]>
http://www.mdpi.com/2079-3197/4/3/28
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.Computation2016-08-0543Article10.3390/computation4030028282079-31972016-08-05doi: 10.3390/computation4030028Vitaly GlushkovMel Levy<![CDATA[Computation, Vol. 4, Pages 27: Automatic Generation of Massively Parallel Codes from ExaSlang]]>
http://www.mdpi.com/2079-3197/4/3/27
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.Computation2016-08-0443Article10.3390/computation4030027272079-31972016-08-04doi: 10.3390/computation4030027Sebastian KuckukHarald Köstler<![CDATA[Computation, Vol. 4, Pages 26: Interaction of Hydrogen with Au Modified by Pd and Rh in View of Electrochemical Applications]]>
http://www.mdpi.com/2079-3197/4/3/26
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).Computation2016-07-2043Article10.3390/computation4030026262079-31972016-07-20doi: 10.3390/computation4030026Fernanda JuarezGerman SoldanoElizabeth SantosHazar GuesmiFrederik TielensTzonka Mineva<![CDATA[Computation, Vol. 4, Pages 25: Predictions of Physicochemical Properties of Ionic Liquids with DFT]]>
http://www.mdpi.com/2079-3197/4/3/25
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.Computation2016-07-1943Article10.3390/computation4030025252079-31972016-07-19doi: 10.3390/computation4030025Karl KaruAnton RuzanovHeigo ErsVladislav IvaništševIsabel Lage-EstebanezJosé García de la Vega<![CDATA[Computation, Vol. 4, Pages 23: Orbital Energy-Based Reaction Analysis of SN2 Reactions]]>
http://www.mdpi.com/2079-3197/4/3/23
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 N2 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.Computation2016-07-0843Article10.3390/computation4030023232079-31972016-07-08doi: 10.3390/computation4030023Takao TsunedaSatoshi MaedaYu HarabuchiRaman Singh<![CDATA[Computation, Vol. 4, Pages 24: On the v-Representabilty Problem in Density Functional Theory: Application to Non-Interacting Systems]]>
http://www.mdpi.com/2079-3197/4/3/24
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.Computation2016-07-0543Article10.3390/computation4030024242079-31972016-07-05doi: 10.3390/computation4030024Markus DäneAntonios Gonis<![CDATA[Computation, Vol. 4, Pages 22: Online Adaptive Local-Global Model Reduction for Flows in Heterogeneous Porous Media]]>
http://www.mdpi.com/2079-3197/4/2/22
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.Computation2016-06-0742Article10.3390/computation4020022222079-31972016-06-07doi: 10.3390/computation4020022Yalchin EfendievEduardo GildinYanfang Yang<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/2/21
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.Computation2016-05-3042Article10.3390/computation4020021212079-31972016-05-30doi: 10.3390/computation4020021Chao-Zhong QinS. HassanizadehLucas Van Oosterhout<![CDATA[Computation, Vol. 4, Pages 20: On the Use of Benchmarks for Multiple Properties]]>
http://www.mdpi.com/2079-3197/4/2/20
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.Computation2016-04-3042Article10.3390/computation4020020202079-31972016-04-30doi: 10.3390/computation4020020Bartolomeo CivalleriRoberto DovesiPascal PernotDavide PrestiAndreas Savin<![CDATA[Computation, Vol. 4, Pages 19: Kinetic and Exchange Energy Densities near the Nucleus]]>
http://www.mdpi.com/2079-3197/4/2/19
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.Computation2016-04-0242Article10.3390/computation4020019192079-31972016-04-02doi: 10.3390/computation4020019Lucian ConstantinEduardo FabianoFabio Della Sala<![CDATA[Computation, Vol. 4, Pages 18: Grand Canonical Monte Carlo Simulation of Nitrogen Adsorption in a Silica Aerogel Model]]>
http://www.mdpi.com/2079-3197/4/2/18
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.Computation2016-04-0142Article10.3390/computation4020018182079-31972016-04-01doi: 10.3390/computation4020018Wen-Li XieZheng-Ji ChenZeng LiWen-Quan Tao<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/2/17
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.Computation2016-03-3042Article10.3390/computation4020017172079-31972016-03-30doi: 10.3390/computation4020017Massimo MarinoDoriano Brogioli<![CDATA[Computation, Vol. 4, Pages 16: Current Issues in Finite-T Density-Functional Theory and Warm-Correlated Matter †]]>
http://www.mdpi.com/2079-3197/4/2/16
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 Te is comparable to the electron Fermi energy EF. 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 Zj. Quasi-equilibria with the ion temperature Ti ≠ Te 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 ne and the one-body ion densities ρj. 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.Computation2016-03-2842Article10.3390/computation4020016162079-31972016-03-28doi: 10.3390/computation4020016M. Dharma-wardana<![CDATA[Computation, Vol. 4, Pages 15: Bonding Strength Effects in Hydro-Mechanical Coupling Transport in Granular Porous Media by Pore-Scale Modeling]]>
http://www.mdpi.com/2079-3197/4/1/15
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.Computation2016-03-0741Article10.3390/computation4010015152079-31972016-03-07doi: 10.3390/computation4010015Zhiqiang ChenChiyu XieYu ChenMoran Wang<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/1/14
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.Computation2016-03-0341Article10.3390/computation4010014142079-31972016-03-03doi: 10.3390/computation4010014Olha TkachukMaria TerebinskayaVictor LobanovAlexei Arbuznikov<![CDATA[Computation, Vol. 4, Pages 13: Direct Numerical Simulation of Turbulent Channel Flow on High-Performance GPU Computing System]]>
http://www.mdpi.com/2079-3197/4/1/13
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.Computation2016-02-2641Article10.3390/computation4010013132079-31972016-02-26doi: 10.3390/computation4010013Giancarlo AlfonsiStefania CilibertiMarco ManciniLeonardo Primavera<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/1/12
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 &gt; θc or the occurrence of corner arc menisci at θ &lt; 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.Computation2016-02-2041Article10.3390/computation4010012122079-31972016-02-20doi: 10.3390/computation4010012Soyoun SonLi ChenQinjun KangDominique DeromeJan Carmeliet<![CDATA[Computation, Vol. 4, Pages 11: Enhancing Computational Precision for Lattice Boltzmann Schemes in Porous Media Flows]]>
http://www.mdpi.com/2079-3197/4/1/11
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.Computation2016-02-1741Article10.3390/computation4010011112079-31972016-02-17doi: 10.3390/computation4010011Farrel GrayEdo Boek<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/1/9
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.Computation2016-02-1641Article10.3390/computation401000992079-31972016-02-16doi: 10.3390/computation4010009Costantino MasciopintoDomenico Palmiotta<![CDATA[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]]>
http://www.mdpi.com/2079-3197/4/1/8
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.Computation2016-02-0641Review10.3390/computation401000882079-31972016-02-06doi: 10.3390/computation4010008John White<![CDATA[Computation, Vol. 4, Pages 7: Applications of Computational Modelling and Simulation of Porous Medium in Tissue Engineering]]>
http://www.mdpi.com/2079-3197/4/1/7
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.Computation2016-02-0641Article10.3390/computation401000772079-31972016-02-06doi: 10.3390/computation4010007Carrie GermanSundararajan Madihally<![CDATA[Computation, Vol. 4, Pages 10: Localized Polycentric Orbital Basis Set for Quantum Monte Carlo Calculations Derived from the Decomposition of Kohn-Sham Optimized Orbitals]]>
http://www.mdpi.com/2079-3197/4/1/10
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.Computation2016-02-0641Article10.3390/computation4010010102079-31972016-02-06doi: 10.3390/computation4010010Claudio AmovilliFranca FlorisAndrea Grisafi<![CDATA[Computation, Vol. 4, Pages 6: Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials]]>
http://www.mdpi.com/2079-3197/4/1/6
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.Computation2016-02-0441Article10.3390/computation401000662079-31972016-02-04doi: 10.3390/computation4010006Claus VoglJuraj Bergman<![CDATA[Computation, Vol. 4, Pages 5: Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case]]>
http://www.mdpi.com/2079-3197/4/1/5
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.Computation2016-01-2641Article10.3390/computation401000552079-31972016-01-26doi: 10.3390/computation4010005Giuliano MallociGiovanni SerraAndrea BosinAttilio Vargiu<![CDATA[Computation, Vol. 4, Pages 4: Acknowledgement to Reviewers of Computation in 2015]]>
http://www.mdpi.com/2079-3197/4/1/4
The editors of Computation would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...]Computation2016-01-2241Editorial10.3390/computation401000442079-31972016-01-22doi: 10.3390/computation4010004 Computation Editorial Office<![CDATA[Computation, Vol. 4, Pages 3: A Test of Various Partial Atomic Charge Models for Computations on Diheteroaryl Ketones and Thioketones]]>
http://www.mdpi.com/2079-3197/4/1/3
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.Computation2016-01-1941Article10.3390/computation401000332079-31972016-01-19doi: 10.3390/computation4010003Piotr Matczak<![CDATA[Computation, Vol. 4, Pages 2: Modeling Groundwater Flow in Heterogeneous Porous Media with YAGMod]]>
http://www.mdpi.com/2079-3197/4/1/2
Modeling flow and transport in porous media requires the management of complexities related both to physical processes and to subsurface heterogeneity. A thorough approach needs a great number of spatially-distributed phenomenological parameters, which are seldom measured in the field. For instance, modeling a phreatic aquifer under high water extraction rates is very challenging, because it requires the simulation of variably-saturated flow. 3D steady groundwater flow is modeled with YAGMod (yet another groundwater flow model), a model based on a finite-difference conservative scheme and implemented in a computer code developed in Fortran90. YAGMod simulates also the presence of partially-saturated or dry cells. The proposed algorithm and other alternative methods developed to manage dry cells in the case of depleted aquifers are analyzed and compared to a simple test. Different approaches yield different solutions, among which, it is not possible to select the best one on the basis of physical arguments. A possible advantage of YAGMod is that no additional non-physical parameter is needed to overcome the numerical difficulties arising to handle drained cells. YAGMod also includes a module that allows one to identify the conductivity field for a phreatic aquifer by solving an inverse problem with the comparison model method.Computation2015-12-2941Article10.3390/computation401000222079-31972015-12-29doi: 10.3390/computation4010002Laura CattaneoAlessandro ComunianGiovanna de FilippisMauro GiudiciChiara Vassena<![CDATA[Computation, Vol. 4, Pages 1: Reduced Numerical Model for Methane Hydrate Formation under Conditions of Variable Salinity. Time-Stepping Variants and Sensitivity]]>
http://www.mdpi.com/2079-3197/4/1/1
In this paper, we consider a reduced computational model of methane hydrate formation in variable salinity conditions, and give details on the discretization and phase equilibria implementation. We describe three time-stepping variants: Implicit, Semi-implicit, and Sequential, and we compare the accuracy and efficiency of these variants depending on the spatial and temporal discretization parameters. We also study the sensitivity of the model to the simulation parameters and in particular to the reduced phase equilibria model.Computation2015-12-2441Article10.3390/computation401000112079-31972015-12-24doi: 10.3390/computation4010001Malgorzata PeszynskaFrancis MedinaWei-Li HongMarta Torres<![CDATA[Computation, Vol. 3, Pages 701-713: Exact Likelihood Calculation under the Infinite Sites Model]]>
http://www.mdpi.com/2079-3197/3/4/701
A key parameter in population genetics is the scaled mutation rate θ = 4 N μ , where N is the effective haploid population size and μ is the mutation rate per haplotype per generation. While exact likelihood inference is notoriously difficult in population genetics, we propose a novel approach to compute a first order accurate likelihood of θ that is based on dynamic programming under the infinite sites model without recombination. The parameter θ may be either constant, i.e., time-independent, or time-dependent, which allows for changes of demography and deviations from neutral equilibrium. For time-independent θ, the performance is compared to the approach in Griffiths and Tavaré’s work “Simulating Probability Distributions in the Coalescent” (Theor. Popul. Biol. 1994, 46, 131–159) that is based on importance sampling and implemented in the “genetree” program. Roughly, the proposed method is computationally fast when n × θ &lt; 100 , where n is the sample size. For time-dependent θ ( t ) , we analyze a simple demographic model with a single change in θ ( t ) . In this case, the ancestral and current θ need to be estimated, as well as the time of change. To our knowledge, this is the first accurate computation of a likelihood in the infinite sites model with non-equilibrium demography.Computation2015-12-1134Article10.3390/computation30407017017132079-31972015-12-11doi: 10.3390/computation3040701Muhammad FaisalAndreas FutschikClaus Vogl<![CDATA[Computation, Vol. 3, Pages 687-700: Molecular Simulation of Shale Gas Adsorption and Diffusion in Clay Nanopores]]>
http://www.mdpi.com/2079-3197/3/4/687
The present work aims to study the adsorption behavior and dynamical properties of CH4 in clay slit pore with or without cation exchange structures at sizes of 1.0 nm–4.0 nm using grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) methods. The adsorption isotherms of CH4 have been investigated by GCMC simulations at different temperatures and various pore sizes. In the montmorillonite (MMT) clays without a cation exchange structure, from the density profile, we find the molecules preferentially adsorb onto the surface, and only an obvious single layer was observed. The general trend within slit pores is that with increasing pore width, the adsorbed amount will increase. However, the larger pores exhibit lower excess density and the smaller pores exhibit higher excess density. The preloaded water will reduce CH4 sorption. The in plane self-diffusion coefficient of CH4 which is investigated by MD simulations combined with Einstein fluid equation increases rapidly with the pore size increasing at low pressure. Under these given conditions, the effect of temperature has little influence on the in-plane self-diffusion coefficient. In the MMT clays with cation exchange structure, cation exchange has little effect on CH4 adsorption and self-diffusion.Computation2015-12-1134Article10.3390/computation30406876877002079-31972015-12-11doi: 10.3390/computation3040687Hongguang SuiJun YaoLei Zhang<![CDATA[Computation, Vol. 3, Pages 670-686: Multiscale Simulations for Coupled Flow and Transport Using the Generalized Multiscale Finite Element Method]]>
http://www.mdpi.com/2079-3197/3/4/670
In this paper, we develop a mass conservative multiscale method for coupled flow and transport in heterogeneous porous media. We consider a coupled system consisting of a convection-dominated transport equation and a flow equation. We construct a coarse grid solver based on the Generalized Multiscale Finite Element Method (GMsFEM) for a coupled system. In particular, multiscale basis functions are constructed based on some snapshot spaces for the pressure and the concentration equations and some local spectral decompositions in the snapshot spaces. The resulting approach uses a few multiscale basis functions in each coarse block (for both the pressure and the concentration) to solve the coupled system. We use the mixed framework, which allows mass conservation. Our main contributions are: (1) the development of a mass conservative GMsFEM for the coupled flow and transport; (2) the development of a robust multiscale method for convection-dominated transport problems by choosing appropriate test and trial spaces within Petrov-Galerkin mixed formulation. We present numerical results and consider several heterogeneous permeability fields. Our numerical results show that with only a few basis functions per coarse block, we can achieve a good approximation.Computation2015-12-1134Article10.3390/computation30406706706862079-31972015-12-11doi: 10.3390/computation3040670Eric ChungYalchin EfendievWing LeungJun Ren<![CDATA[Computation, Vol. 3, Pages 657-669: Optical Properties of Silicon-Rich Silicon Nitride (SixNyHz) from First Principles]]>
http://www.mdpi.com/2079-3197/3/4/657
The real and imaginary parts of the complex refractive index of SixNyHz have been calculated from first principles. Optical spectra for reflectivity, absorption coefficient, energy-loss function (ELF), and refractive index were obtained. The results for Si3N4 are in agreement with the available theoretical and experimental results. To understand the electron energy loss mechanism in Si-rich silicon nitride, the influence of the Si/N ratio, the positions of the access Si atoms, and H in and on the surface of the ELF have been investigated. It has been found that all defects, such as dangling bonds in the bulk and surfaces, increase the intensity of the ELF in the low energy range (below 10 eV). H in the bulk and on the surface has a healing effect, which can reduce the intensity of the loss peaks by saturating the dangling bonds. Electronic structure analysis has confirmed the origin of the changes in the ELF. It has demonstrated that the changes in ELF are not only affected by the composition but also by the microstructures of the materials. The results can be used to tailor the optical properties, in this case the ELF of Si-rich Si3N4, which is essential for secondary electron emission applications.Computation2015-12-0834Article10.3390/computation30406576576692079-31972015-12-08doi: 10.3390/computation3040657Shu TaoAnne TheulingsVioleta ProdanovićJohn SmedleyHarry van der Graaf<![CDATA[Computation, Vol. 3, Pages 616-656: Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations]]>
http://www.mdpi.com/2079-3197/3/4/616
Ionization potentials (IPs) and electron affinities (EAs) are important quantities input into most models for calculating the open-circuit voltage (Voc) of organic solar cells. We assess the semi-empirical density-functional tight-binding (DFTB) method with the third-order self-consistent charge (SCC) correction and the 3ob parameter set (the third-order DFTB (DFTB3) organic and biochemistry parameter set) against experiments (for smaller molecules) and against first-principles GW (Green’s function, G, times the screened potential, W) calculations (for larger molecules of interest in organic electronics) for the calculation of IPs and EAs. Since GW calculations are relatively new for molecules of this size, we have also taken care to validate these calculations against experiments. As expected, DFTB is found to behave very much like density-functional theory (DFT), but with some loss of accuracy in predicting IPs and EAs. For small molecules, the best results were found with ΔSCF (Δ self-consistent field) SCC-DFTB calculations for first IPs (good to ± 0.649 eV). When considering several IPs of the same molecule, it is convenient to use the negative of the orbital energies (which we refer to as Koopmans’ theorem (KT) IPs) as an indication of trends. Linear regression analysis shows that KT SCC-DFTB IPs are nearly as accurate as ΔSCF SCC-DFTB eigenvalues (± 0.852 eV for first IPs, but ± 0.706 eV for all of the IPs considered here) for small molecules. For larger molecules, SCC-DFTB was also the ideal choice with IP/EA errors of ± 0.489/0.740 eV from ΔSCF calculations and of ± 0.326/0.458 eV from (KT) orbital energies. Interestingly, the linear least squares fit for the KT IPs of the larger molecules also proves to have good predictive value for the lower energy KT IPs of smaller molecules, with significant deviations appearing only for IPs of 15–20 eV or larger. We believe that this quantitative analysis of errors in SCC-DFTB IPs and EAs may be of interest to other researchers interested in DFTB investigation of large and complex problems, such as those encountered in organic electronics.Computation2015-12-0434Article10.3390/computation30406166166562079-31972015-12-04doi: 10.3390/computation3040616Ala DarghouthMark CasidaWalid TaoualiKamel AlimiMathias LjungbergPeter KovalDaniel Sánchez-PortalDietrich Foerster<![CDATA[Computation, Vol. 3, Pages 600-615: An Incompressible, Depth-Averaged Lattice Boltzmann Method for Liquid Flow in Microfluidic Devices with Variable Aperture]]>
http://www.mdpi.com/2079-3197/3/4/600
Two-dimensional (2D) pore-scale models have successfully simulated microfluidic experiments of aqueous-phase flow with mixing-controlled reactions in devices with small aperture. A standard 2D model is not generally appropriate when the presence of mineral precipitate or biomass creates complex and irregular three-dimensional (3D) pore geometries. We modify the 2D lattice Boltzmann method (LBM) to incorporate viscous drag from the top and bottom microfluidic device (micromodel) surfaces, typically excluded in a 2D model. Viscous drag from these surfaces can be approximated by uniformly scaling a steady-state 2D velocity field at low Reynolds number. We demonstrate increased accuracy by approximating the viscous drag with an analytically-derived body force which assumes a local parabolic velocity profile across the micromodel depth. Accuracy of the generated 2D velocity field and simulation permeability have not been evaluated in geometries with variable aperture. We obtain permeabilities within approximately 10% error and accurate streamlines from the proposed 2D method relative to results obtained from 3D simulations. In addition, the proposed method requires a CPU run time approximately 40 times less than a standard 3D method, representing a significant computational benefit for permeability calculations.Computation2015-11-2434Article10.3390/computation30406006006152079-31972015-11-24doi: 10.3390/computation3040600Artin LaleianAlbert ValocchiCharles Werth<![CDATA[Computation, Vol. 3, Pages 586-599: Dominant Strategies of Quantum Games on Quantum Periodic Automata]]>
http://www.mdpi.com/2079-3197/3/4/586
Game theory and its quantum extension apply in numerous fields that affect people’s social, political, and economical life. Physical limits imposed by the current technology used in computing architectures (e.g., circuit size) give rise to the need for novel mechanisms, such as quantum inspired computation. Elements from quantum computation and mechanics combined with game-theoretic aspects of computing could open new pathways towards the future technological era. This paper associates dominant strategies of repeated quantum games with quantum automata that recognize infinite periodic inputs. As a reference, we used the PQ-PENNY quantum game where the quantum strategy outplays the choice of pure or mixed strategy with probability 1 and therefore the associated quantum automaton accepts with probability 1. We also propose a novel game played on the evolution of an automaton, where players’ actions and strategies are also associated with periodic quantum automata.Computation2015-11-2034Article10.3390/computation30405865865992079-31972015-11-20doi: 10.3390/computation3040586Konstantinos GiannakisChristos PapalitsasKalliopi KastampolidouAlexandros SinghTheodore Andronikos<![CDATA[Computation, Vol. 3, Pages 574-585: A Comparative Density Functional Theory and Density Functional Tight Binding Study of Phases of Nitrogen Including a High Energy Density Material N8]]>
http://www.mdpi.com/2079-3197/3/4/574
We present a comparative dispersion-corrected Density Functional Theory (DFT) and Density Functional Tight Binding (DFTB-D) study of several phases of nitrogen, including the well-known alpha, beta, and gamma phases as well as recently discovered highly energetic phases: covalently bound cubic gauche (cg) nitrogen and molecular (vdW-bound) N8 crystals. Among several tested parametrizations of N–N interactions for DFTB, we identify only one that is suitable for modeling of all these phases. This work therefore establishes the applicability of DFTB-D to studies of phases, including highly metastable phases, of nitrogen, which will be of great use for modelling of dynamics of reactions involving these phases, which may not be practical with DFT due to large required space and time scales. We also derive a dispersion-corrected DFT (DFT-D) setup (atom-centered basis parameters and Grimme dispersion parameters) tuned for accurate description simultaneously of several nitrogen allotropes including covalently and vdW-bound crystals and including high-energy phases.Computation2015-11-1134Article10.3390/computation30405745745852079-31972015-11-11doi: 10.3390/computation3040574Nicholas CapelDevang BharaniaSergei Manzhos<![CDATA[Computation, Vol. 3, Pages 558-573: Effective Thermal Conductivity of MOF-5 Powder under a Hydrogen Atmosphere]]>
http://www.mdpi.com/2079-3197/3/4/558
Effective thermal conductivity is an important thermophysical property in the design of metal-organic framework-5 (MOF-5)-based hydrogen storage tanks. A modified thermal conductivity model is built by coupling a theoretical model with the grand canonical Monte Carlo simulation (GCMC) to predict the effect of the H2 adsorption process on the effective thermal conductivity of a MOF-5 powder bed at pressures ranging from 0.01 MPa to 50 MPa and temperatures ranging from 273.15 K to 368.15 K. Results show that the mean pore diameter of the MOF-5 crystal decreases with an increase in pressure and increases with an increase in temperature. The thermal conductivity of the adsorbed H2 increases with an increased amount of H2 adsorption. The effective thermal conductivity of the MOF-5 crystal is significantly enhanced by the H2 adsorption at high pressure and low temperature. The effective thermal conductivity of the MOF-5 powder bed increases with an increase in pressure and remains nearly unchanged with an increase in temperature. The thermal conductivity of the MOF-5 powder bed increases linearly with the decreased porosity and increased thermal conductivity of the skeleton of the MOF-5 crystal. The variation in the effective thermal conductivities of the MOF-5 crystals and bed mainly results from the thermal conductivities of the gaseous and adsorption phases.Computation2015-11-0634Article10.3390/computation30405585585732079-31972015-11-06doi: 10.3390/computation3040558Hui WangZhiguo QuWen ZhangWenquan Tao<![CDATA[Computation, Vol. 3, Pages 541-557: Numerical Simulation of Fluid-Solid Coupling in Fractured Porous Media with Discrete Fracture Model and Extended Finite Element Method]]>
http://www.mdpi.com/2079-3197/3/4/541
Fluid-solid coupling is ubiquitous in the process of fluid flow underground and has a significant influence on the development of oil and gas reservoirs. To investigate these phenomena, the coupled mathematical model of solid deformation and fluid flow in fractured porous media is established. In this study, the discrete fracture model (DFM) is applied to capture fluid flow in the fractured porous media, which represents fractures explicitly and avoids calculating shape factor for cross flow. In addition, the extended finite element method (XFEM) is applied to capture solid deformation due to the discontinuity caused by fractures. More importantly, this model captures the change of fractures aperture during the simulation, and then adjusts fluid flow in the fractures. The final linear equation set is derived and solved for a 2D plane strain problem. Results show that the combination of discrete fracture model and extended finite element method is suited for simulating coupled deformation and fluid flow in fractured porous media.Computation2015-10-3034Article10.3390/computation30405415415572079-31972015-10-30doi: 10.3390/computation3040541Qingdong ZengJun Yao<![CDATA[Computation, Vol. 3, Pages 528-540: A Scale Invariant Distribution of the Prime Numbers]]>
http://www.mdpi.com/2079-3197/3/4/528
The irregular distribution of prime numbers amongst the integers has found multiple uses, from engineering applications of cryptography to quantum theory. The degree to which this distribution can be predicted thus has become a subject of current interest. Here, we present a computational analysis of the deviations between the actual positions of the prime numbers and their predicted positions from Riemann’s counting formula, focused on the variance function of these deviations from sequential enumerative bins. We show empirically that these deviations can be described by a class of probabilistic models known as the Tweedie exponential dispersion models that are characterized by a power law relationship between the variance and the mean, known by biologists as Taylor’s power law and by engineers as fluctuation scaling. This power law behavior of the prime number deviations is remarkable in that the same behavior has been found within the distribution of genes and single nucleotide polymorphisms (SNPs) within the human genome, the distribution of animals and plants within their habitats, as well as within many other biological and physical processes. We explain the common features of this behavior through a statistical convergence effect related to the central limit theorem that also generates 1/f noise.Computation2015-10-2834Article10.3390/computation30405285285402079-31972015-10-28doi: 10.3390/computation3040528Wayne KendalBent Jørgensen<![CDATA[Computation, Vol. 3, Pages 509-527: CFD and Experimental Study on the Effect of Progressive Heating on Fluid Flow inside a Thermal Wind Tunnel]]>
http://www.mdpi.com/2079-3197/3/4/509
A detailed Computational Fluid Dynamics (CFD) and experimental investigation into characterizing the fluid flow and thermal profiles in a wind tunnel was carried out, highlighting the effect of progressive heating on the non-uniformity flow profile of air. Using controllable electrical heating elements, the operating temperatures in the test-section were gradually increased in order to determine its influence on the subsequent velocity and thermal profiles found inside the test-section. The numerical study was carried out using CFD FLUENT code, alongside validating the experimental results. Good correlation was observed as the comparison yielded a mean error of 6.4% for the air velocity parameter and 2.3% for the air temperature parameter between the two techniques. The good correlation established between the numerically predicted and experimentally tested results identified broad scope for using the advanced computational capabilities of CFD applicable to the thermal modeling of wind tunnels. For a constant temperature process, the non-uniformity and turbulence intensity in the test section was 0.9% and 0.5%, which is under the recommended guidelines for wind tunnels. The findings revealed that the increase in temperature from 20 °C to 50 °C reduced the velocity by 15.2% inside the test section.Computation2015-10-2134Article10.3390/computation30405095095272079-31972015-10-21doi: 10.3390/computation3040509Hassam ChaudhryJohn CalautitBen HughesLik Sim<![CDATA[Computation, Vol. 3, Pages 479-508: Applicability of URANS and DES Simulations of Flow Past Rectangular Cylinders and Bridge Sections]]>
http://www.mdpi.com/2079-3197/3/3/479
This paper discusses the results of computational fluid dynamics simulations carried out for rectangular cylinders with various side ratios of interest for many civil engineering structures. A bridge deck of common cross-section geometry was also considered. Unsteady Reynolds-averaged Navier–Stokes (URANS) equations were solved in conjunction with either an eddy viscosity or a linearized explicit algebraic Reynolds stress model. The analysis showed that for the case studies considered, the 2D URANS approach was able to give reasonable results if coupled with an advanced turbulence model and a suitable computational mesh. The simulations even reproduced, at least qualitatively, complex phenomena observed in the wind tunnel, such as Reynolds number effects for a sharp-edged geometry. The study focused both on stationary and harmonically oscillating bodies. For the latter, self-excited forces and flutter derivatives were calculated and compared to experimental data. In the particular case of a benchmark rectangular 5:1 cylinder, 3D detached eddy simulations were also carried out, highlighting the improvement in the accuracy of the results with respect to both 2D and 3D URANS calculations. All of the computations were performed with the Tau code, a non-commercial unstructured solver developed by the German Aerospace Center.Computation2015-09-1833Article10.3390/computation30304794795082079-31972015-09-18doi: 10.3390/computation3030479Claudio Mannini<![CDATA[Computation, Vol. 3, Pages 444-478: Towards Online Visualization and Interactive Monitoring of Real-Time CFD Simulations on Commodity Hardware]]>
http://www.mdpi.com/2079-3197/3/3/444
Real-time rendering in the realm of computational fluid dynamics (CFD) in particular and scientific high performance computing (HPC) in general is a comparably young field of research, as the complexity of most problems with practical relevance is too high for a real-time numerical simulation. However, recent advances in HPC and the development of very efficient numerical techniques allow running first optimized numerical simulations in or near real-time, which in return requires integrated and optimized visualization techniques that do not affect performance. In this contribution, we present concepts, implementation details and several application examples of a minimally-invasive, efficient visualization tool for the interactive monitoring of 2D and 3D turbulent flow simulations on commodity hardware. The numerical simulations are conducted with ELBE, an efficient lattice Boltzmann environment based on NVIDIA CUDA (Compute Unified Device Architecture), which provides optimized numerical kernels for 2D and 3D computational fluid dynamics with fluid-structure interactions and turbulence.Computation2015-09-1133Article10.3390/computation30304444444782079-31972015-09-11doi: 10.3390/computation3030444Nils KolihaChristian JanßenThomas Rung<![CDATA[Computation, Vol. 3, Pages 427-443: Computational Modeling of Teaching and Learning through Application of Evolutionary Algorithms]]>
http://www.mdpi.com/2079-3197/3/3/427
Within the mind, there are a myriad of ideas that make sense within the bounds of everyday experience, but are not reflective of how the world actually exists; this is particularly true in the domain of science. Classroom learning with teacher explanation are a bridge through which these naive understandings can be brought in line with scientific reality. The purpose of this paper is to examine how the application of a Multiobjective Evolutionary Algorithm (MOEA) can work in concert with an existing computational-model to effectively model critical-thinking in the science classroom. An evolutionary algorithm is an algorithm that iteratively optimizes machine learning based computational models. The research question is, does the application of an evolutionary algorithm provide a means to optimize the Student Task and Cognition Model (STAC-M) and does the optimized model sufficiently represent and predict teaching and learning outcomes in the science classroom? Within this computational study, the authors outline and simulate the effect of teaching on the ability of a “virtual” student to solve a Piagetian task. Using the Student Task and Cognition Model (STAC-M) a computational model of student cognitive processing in science class developed in 2013, the authors complete a computational experiment which examines the role of cognitive retraining on student learning. Comparison of the STAC-M and the STAC-M with inclusion of the Multiobjective Evolutionary Algorithm shows greater success in solving the Piagetian science-tasks post cognitive retraining with the Multiobjective Evolutionary Algorithm. This illustrates the potential uses of cognitive and neuropsychological computational modeling in educational research. The authors also outline the limitations and assumptions of computational modeling.Computation2015-09-0233Article10.3390/computation30304274274432079-31972015-09-02doi: 10.3390/computation3030427Richard LambJoshua Premo<![CDATA[Computation, Vol. 3, Pages 386-426: Numerical Simulations of Wave-Induced Flow Fields around Large-Diameter Surface-Piercing Vertical Circular Cylinder]]>
http://www.mdpi.com/2079-3197/3/3/386
A computational analysis is performed on the diffraction of water waves induced by large-diameter, surface-piercing, vertical circular cylinder. With reference to linear-wave cases, the phenomenon is preliminarly considered in terms of velocity potential, a simplified theoretical framework in which both hypotheses of inviscid fluid and irrotational flow are incorporated. Then, and as a first-approximation analysis, the Euler equations in primitive variables are considered (a framework in which the fluid is still handled as inviscid, but the field can be rotational). Finally, the real-fluid behavior is analyzed, by numerically integrating the full Navier-Stokes equations (viscous fluid and rotational field) in their velocity-pressure formulation, by following the approach of the Direct Numerical Simulation (DNS, no models are used for the fluctuating portion of the velocity field). For further investigation of the flow fields, the swirling-strength criterion for flow-structure extraction, and the Karhunen-Loève (KL) decomposition technique for the extraction of the most energetic flow modes respectively, are applied to the computed fields. It is found that remarkable differences exist between the wave-induced fields, as derived within the different computing frameworks tested.Computation2015-08-2833Article10.3390/computation30303863864262079-31972015-08-28doi: 10.3390/computation3030386Giancarlo Alfonsi<![CDATA[Computation, Vol. 3, Pages 354-385: Validation of the GPU-Accelerated CFD Solver ELBE for Free Surface Flow Problems in Civil and Environmental Engineering]]>
http://www.mdpi.com/2079-3197/3/3/354
This contribution is dedicated to demonstrating the high potential and manifold applications of state-of-the-art computational fluid dynamics (CFD) tools for free-surface flows in civil and environmental engineering. All simulations were performed with the academic research code ELBE (efficient lattice boltzmann environment, http://www.tuhh.de/elbe). The ELBE code follows the supercomputing-on-the-desktop paradigm and is especially designed for local supercomputing, without tedious accesses to supercomputers. ELBE uses graphics processing units (GPU) to accelerate the computations and can be used in a single GPU-equipped workstation of, e.g., a design engineer. The code has been successfully validated in very different fields, mostly related to naval architecture and mechanical engineering. In this contribution, we give an overview of past and present applications with practical relevance for civil engineers. The presented applications are grouped into three major categories: (i) tsunami simulations, considering wave propagation, wave runup, inundation and debris flows; (ii) dam break simulations; and (iii) numerical wave tanks for the calculation of hydrodynamic loads on fixed and moving bodies. This broad range of applications in combination with accurate numerical results and very competitive times to solution demonstrates that modern CFD tools in general, and the ELBE code in particular, can be a helpful design tool for civil and environmental engineers.Computation2015-07-0733Article10.3390/computation30303543543852079-31972015-07-07doi: 10.3390/computation3030354Christian JanßenDennis MierkeMicha ÜberrückSilke GralherThomas Rung<![CDATA[Computation, Vol. 3, Pages 336-353: In Silico Comparison of the Hemicelluloses Xyloglucan and Glucuronoarabinoxylan in Protecting Cellulose from Degradation]]>
http://www.mdpi.com/2079-3197/3/3/336
We used a previously developed simulation model of a plant cell wall and its enzymatic degradation to compare the abilities of two hemicelluloses, glucuronoarabinoxylan (GAX) and xyloglucan (XG), to protect cellulose microfibrils (CMFs) from attack by cellulose-degrading enzymes. Additionally, we investigated the effect of XG abundance on the degradation rate of CMFs in the presence of the same enzymes. Simulations were run using hypothetical cell-wall compositions in which the numbers and arrangement of CMFs and (1,3;1,4)-β-glucan were kept constant, but the proportions of GAX and XG were altered. Scenarios considered walls with low and equal proportions of either GAX or XG, and also low, medium and high proportions of XG in the absence of GAX. The rate of CMF degradation was much lower in walls with GAX than walls with XG, except for early in the simulation when the reverse held, suggesting that XGs were protecting CMFs by competitive inhibition. Increasing XG content reduced both the degradation rate of CMFs and the percent of XG degraded, indicating that activity of enzymes decreased with XG density despite XG being degradable. Glucose oligosaccharide breakdown products were analysed on the basis of the originating polysaccharide and their degree of polymerisation (DP). The presence of GAX as opposed to equal amounts of XG had some significant effects on the amount and profile of breakdown products from XG and CMFs.Computation2015-07-0633Article10.3390/computation30303363363532079-31972015-07-06doi: 10.3390/computation3030336Indrakumar VetharaniamMartin UpsdellWilliam KellyGraeme AttwoodChristina MoonPhilip Harris<![CDATA[Computation, Vol. 3, Pages 326-335: Fast Computation of the Non-Central Chi Square PDF Outside the HDR Under a Requisite Precision Constraint]]>
http://www.mdpi.com/2079-3197/3/2/326
Computation of the non-central chi square probability density function is encountered in diverse fields of applied statistics and engineering. The distribution is commonly computed as a Poisson mixture of central chi square densities, where the terms of the sum are computed starting with the integer nearest the non-centrality parameter. However, for computation of the values in either tail region these terms are not the most significant and starting with them results in an increased computational load without a corresponding increase in accuracy. The most significant terms are shown to be a function of both the non-centrality parameter, the degree of freedom and the point of evaluation. A computationally simple approximate solution to the location of the most significant terms as well as the exact solution based on a Newton–Raphson iteration is presented. A quadratic approximation of the interval of summation is also developed in order to meet a requisite number of significant digits of accuracy. Computationally efficient recursions are used over these improved intervals. The method provides a means of computing the non-central chi square probability density function to a requisite accuracy as a Poisson mixture over all domains of interest.Computation2015-06-1932Article10.3390/computation30203263263352079-31972015-06-19doi: 10.3390/computation3020326Paul Gendron<![CDATA[Computation, Vol. 3, Pages 299-325: On Roof Geometry for Urban Wind Energy Exploitation in High-Rise Buildings]]>
http://www.mdpi.com/2079-3197/3/2/299
The European program HORIZON2020 aims to have 20% of electricity produced by renewable sources. The building sector represents 40% of the European Union energy consumption. Reducing energy consumption in buildings is therefore a priority for energy efficiency. The present investigation explores the most adequate roof shapes compatible with the placement of different types of small wind energy generators on high-rise buildings for urban wind energy exploitation. The wind flow around traditional state-of-the-art roof shapes is considered. In addition, the influence of the roof edge on the wind flow on high-rise buildings is analyzed. These geometries are investigated, both qualitatively and quantitatively, and the turbulence intensity threshold for horizontal axis wind turbines is considered. The most adequate shapes for wind energy exploitation are identified, studying vertical profiles of velocity, turbulent kinetic energy and turbulence intensity. Curved shapes are the most interesting building roof shapes from the wind energy exploitation point of view, leading to the highest speed-up and the lowest turbulence intensity.Computation2015-06-1032Article10.3390/computation30202992993252079-31972015-06-10doi: 10.3390/computation3020299Francisco Toja-SilvaCarlos PeraltaOscar Lopez-GarciaJorge NavarroIgnacio Cruz<![CDATA[Computation, Vol. 3, Pages 285-298: Computational Recognition of RNA Splice Sites by Exact Algorithms for the Quadratic Traveling Salesman Problem]]>
http://www.mdpi.com/2079-3197/3/2/285
One fundamental problem of bioinformatics is the computational recognition of DNA and RNA binding sites. Given a set of short DNA or RNA sequences of equal length such as transcription factor binding sites or RNA splice sites, the task is to learn a pattern from this set that allows the recognition of similar sites in another set of DNA or RNA sequences. Permuted Markov (PM) models and permuted variable length Markov (PVLM) models are two powerful models for this task, but the problem of finding an optimal PM model or PVLM model is NP-hard. While the problem of finding an optimal PM model or PVLM model of order one is equivalent to the traveling salesman problem (TSP), the problem of finding an optimal PM model or PVLM model of order two is equivalent to the quadratic TSP (QTSP). Several exact algorithms exist for solving the QTSP, but it is unclear if these algorithms are capable of solving QTSP instances resulting from RNA splice sites of at least 150 base pairs in a reasonable time frame. Here, we investigate the performance of three exact algorithms for solving the QTSP for ten datasets of splice acceptor sites and splice donor sites of five different species and find that one of these algorithms is capable of solving QTSP instances of up to 200 base pairs with a running time of less than two days.Computation2015-06-0332Article10.3390/computation30202852852982079-31972015-06-03doi: 10.3390/computation3020285Anja FischerFrank FischerGerold JägerJens KeilwagenPaul MolitorIvo Grosse<![CDATA[Computation, Vol. 3, Pages 274-284: Effects of a Sprinkler on Evacuation Dynamics in Fire]]>
http://www.mdpi.com/2079-3197/3/2/274
A fire in an enclosed space, such as a room in a building, is generally called a compartment fire. To prevent the compartment fire, a sprinkler for first-aid fire-fighting is installed in rooms. However, it is difficult to determine the degree to which smoke generation and the fire spreading will be inhibited when sprinklers are on. In particular, demonstrating evacuation behavior assuming an actual fire is impossible. In this study, we evaluated an effectiveness of the sprinkler by numerical simulations. To consider evacuation dynamics, a real-coded cellular automata (RCA) was used, where we can freely set the direction and velocity of an evacuee based on a floor field model. To consider the situation in the room fire, we used a simulator called Fire Dynamics Simulator (FDS). Two cases with and without the sprinkler were compared to see the validity of the sprinkler on evacuation dynamics. The effect of smoke and the expansion of the fire-spreading region were discussed. Results show that, since the fire-spreading region disappears when the sprinkler is actuated, the evacuation time decreases. Even though the sprinkler is actuated, the smoke generated at the beginning of a fire diffuses inside the whole room. However, the duration of evacuees being overwhelmed by smoke is less, because the amount of smoke generated by the pyrolysis reaction is much decreased.Computation2015-06-0332Article10.3390/computation30202742742842079-31972015-06-03doi: 10.3390/computation3020274Kazuhiro YamamotoYuki TakeuchiShinnosuke Nishiki<![CDATA[Computation, Vol. 3, Pages 262-273: LES: Unsteady Atmospheric Turbulent Layer Inlet. A Precursor Method Application and Its Quality Check]]>
http://www.mdpi.com/2079-3197/3/2/262
The motivation of this work is to bridge the gap between experimental approaches in wind tunnel testing and numerical computations, in the field of structural design against strong winds. This paper focuses on the generation of an unsteady flow field, representative of a natural wind field, but still compatible with Computational Fluid Dynamics inlet requirements. A simple and “naive” procedure is explained, and the results are in good agreement with some international standards.Computation2015-05-2632Article10.3390/computation30202622622732079-31972015-05-26doi: 10.3390/computation3020262Julien Berthaut-GerentesDidier Delaunay<![CDATA[Computation, Vol. 3, Pages 235-261: Engineering-Based Thermal CFD Simulations on Massive Parallel Systems]]>
http://www.mdpi.com/2079-3197/3/2/235
The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this paper, we present a hierarchical data structure for massive parallel computations that supports the coupling of a Navier–Stokes-based fluid flow code with the Boussinesq approximation in order to address complex thermal scenarios for energy-related assessments. The newly designed data structure is specifically designed with the idea of interactive data exploration and visualization during runtime of the simulation code; a major shortcoming of traditional high-performance computing (HPC) simulation codes. We further show and discuss speed-up values obtained on one of Germany’s top-ranked supercomputers with up to 140,000 processes and present simulation results for different engineering-based thermal problems.Computation2015-05-2232Article10.3390/computation30202352352612079-31972015-05-22doi: 10.3390/computation3020235Jérôme FrischRalf-Peter MundaniErnst RankChristoph van Treeck<![CDATA[Computation, Vol. 3, Pages 222-234: Computational Approach to 3D Modeling of the Lymph Node Geometry]]>
http://www.mdpi.com/2079-3197/3/2/222
In this study we present a computational approach to the generation of the major geometric structures of an idealized murine lymph node (LN). In this generation, we consider the major compartments such as the subcapsular sinus, B cell follicles, trabecular and medullar sinuses, blood vessels and the T cell zone with a primary focus on the fibroblastic reticular cell (FRC) network. Confocal microscopy data of LN macroscopic structures and structural properties of the FRC network have been generated and utilized in the present model. The methodology sets a library of modules that can be used to assemble a solid geometric LN model and subsequently generate an adaptive mesh model capable of implementing transport phenomena. Overall, based on the use of high-resolution confocal microscopy and morphological analysis of cell 3D reconstructions, we have developed a computational model of the LN geometry, suitable for further investigation in studies of fluid transport and cell migration in this immunologically essential organ.Computation2015-05-2232Communication10.3390/computation30202222222342079-31972015-05-22doi: 10.3390/computation3020222Alexey KislitsynRostislav SavinkovMario NovkovicLucas OnderGennady Bocharov<![CDATA[Computation, Vol. 3, Pages 197-221: Simulation Frameworks for Morphogenetic Problems]]>
http://www.mdpi.com/2079-3197/3/2/197
Morphogenetic modelling and simulation help to understand the processes by which the form and shapes of organs (organogenesis) and organisms (embryogenesis) emerge. This requires two mutually coupled entities: the biomolecular signalling network and the tissue. Whereas the modelling of the signalling has been discussed and used in a multitude of works, the realistic modelling of the tissue has only started on a larger scale in the last decade. Here, common tissue modelling techniques are reviewed. Besides the continuum approach, the principles and main applications of the spheroid, vertex, Cellular Potts, Immersed Boundary and Subcellular Element models are discussed in detail. In recent years, many software frameworks, implementing the aforementioned methods, have been developed. The most widely used frameworks and modelling markup languages and standards are presented.Computation2015-04-2432Review10.3390/computation30201971972212079-31972015-04-24doi: 10.3390/computation3020197Simon Tanaka<![CDATA[Computation, Vol. 3, Pages 177-196: A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree]]>
http://www.mdpi.com/2079-3197/3/2/177
There are numerous phylogenetic reconstruction methods and models available—but which should you use and why? Important considerations in phylogenetic analyses include data quality, structure, signal, alignment length and sampling. If poorly modelled, variation in rates of change across proteins and across lineages can lead to incorrect phylogeny reconstruction which can then lead to downstream misinterpretation of the underlying data. The risk of choosing and applying an inappropriate model can be reduced with some critical yet straightforward steps outlined in this paper. We use the question of the position of the root of placental mammals as our working example to illustrate the topological impact of model misspecification. Using this case study we focus on using models in a Bayesian framework and we outline the steps involved in identifying and assessing better fitting models for specific datasets.Computation2015-04-1532Article10.3390/computation30201771771962079-31972015-04-15doi: 10.3390/computation3020177Raymond MoranClaire MorganMary O'Connell<![CDATA[Computation, Vol. 3, Pages 150-176: Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response]]>
http://www.mdpi.com/2079-3197/3/2/150
Computational and mathematical modeling is important in support of a better understanding of complex behavior in biology. For the investigation of biological systems, researchers have used computers to construct, verify, and validate models that describe the mechanisms behind biological processes in multi-scale representations. In this paper we combine Petri net models that represent the mycobacterial infection process and innate immune response at various levels of organization, from molecular interaction to granuloma dissemination. In addition to the conventional graphical representation of the Petri net, the outcome of the model is projected onto a 3D model representing the zebrafish embryo. In this manner we provide a visualization of the process in a simulation framework that portrays the infection in the living system.Computation2015-04-0832Article10.3390/computation30201501501762079-31972015-04-08doi: 10.3390/computation3020150Rafael CarvalhoJeroen van den HeuvelJetty KleijnFons Verbeek<![CDATA[Computation, Vol. 3, Pages 128-149: CFD Simulation and Optimisation of a Low Energy Ventilation and Cooling System]]>
http://www.mdpi.com/2079-3197/3/2/128
Mechanical Heating Ventilation and Air-Conditioning (HVAC) systems account for 60% of the total energy consumption of buildings. As a sector, buildings contributes about 40% of the total global energy demand. By using passive technology coupled with natural ventilation from wind towers, significant amounts of energy can be saved, reducing the emissions of greenhouse gases. In this study, the development of Computational Fluid Dynamics (CFD) analysis in aiding the development of wind towers was explored. Initial concepts of simple wind tower mechanics to detailed design of wind towers which integrate modifications specifically to improve the efficiency of wind towers were detailed. From this, using CFD analysis, heat transfer devices were integrated into a wind tower to provide cooling for incoming air, thus negating the reliance on mechanical HVAC systems. A commercial CFD code Fluent was used in this study to simulate the airflow inside the wind tower model with the heat transfer devices. Scaled wind tunnel testing was used to validate the computational model. The airflow supply velocity was measured and compared with the numerical results and good correlation was observed. Additionally, the spacing between the heat transfer devices was varied to optimise the performance. The technology presented here is subject to a patent application (PCT/GB2014/052263).Computation2015-04-0232Article10.3390/computation30201281281492079-31972015-04-02doi: 10.3390/computation3020128John CalautitDominic O'ConnorPolytimi SofotasiouBen Hughes<![CDATA[Computation, Vol. 3, Pages 114-127: Evolution by Pervasive Gene Fusion in Antibiotic Resistance and Antibiotic Synthesizing Genes]]>
http://www.mdpi.com/2079-3197/3/2/114
Phylogenetic (tree-based) approaches to understanding evolutionary history are unable to incorporate convergent evolutionary events where two genes merge into one. In this study, as exemplars of what can be achieved when a tree is not assumed a priori, we have analysed the evolutionary histories of polyketide synthase genes and antibiotic resistance genes and have shown that their history is replete with convergent events as well as divergent events. We demonstrate that the overall histories of these genes more closely resembles the remodelling that might be seen with the children’s toy Lego, than the standard model of the phylogenetic tree. This work demonstrates further that genes can act as public goods, available for re-use and incorporation into other genetic goods.Computation2015-03-2632Article10.3390/computation30201141141272079-31972015-03-26doi: 10.3390/computation3020114Orla ColemanRuth HoganNicole McGoldrickNiamh RuddenJames McInerney<![CDATA[Computation, Vol. 3, Pages 99-113: Evolutionary Dynamics in Gene Networks and Inference Algorithms]]>
http://www.mdpi.com/2079-3197/3/1/99
Dynamical interactions among sets of genes (and their products) regulate developmental processes and some dynamical diseases, like cancer. Gene regulatory networks (GRNs) are directed networks that define interactions (links) among different genes/proteins involved in such processes. Genetic regulation can be modified during the time course of the process, which may imply changes in the nodes activity that leads the system from a specific state to a different one at a later time (dynamics). How the GRN modifies its topology, to properly drive a developmental process, and how this regulation was acquired across evolution are questions that the evolutionary dynamics of gene networks tackles. In the present work we review important methodology in the field and highlight the combination of these methods with evolutionary algorithms. In recent years, this combination has become a powerful tool to fit models with the increasingly available experimental data.Computation2015-03-1331Review10.3390/computation3010099991132079-31972015-03-13doi: 10.3390/computation3010099Daniel Aguilar-HidalgoMaría LemosAntonio Córdoba<![CDATA[Computation, Vol. 3, Pages 72-98: Use of CMEIAS Image Analysis Software to Accurately Compute Attributes of Cell Size, Morphology, Spatial Aggregation and Color Segmentation that Signify in Situ Ecophysiological Adaptations in Microbial Biofilm Communities]]>
http://www.mdpi.com/2079-3197/3/1/72
In this review, we describe computational features of computer-assisted microscopy that are unique to the Center for Microbial Ecology Image Analysis System (CMEIAS) software, and examples illustrating how they can be used to gain ecophysiological insights into microbial adaptations occurring at micrometer spatial scales directly relevant to individual cells occupying their ecological niches in situ. These features include algorithms that accurately measure (1) microbial cell length relevant to avoidance of protozoan bacteriovory; (2) microbial biovolume body mass relevant to allometric scaling and local apportionment of growth-supporting nutrient resources; (3) pattern recognition rules for morphotype classification of diverse microbial communities relevant to their enhanced fitness for success in the particular habitat; (4) spatial patterns of coaggregation that reveal the local intensity of cooperative vs. competitive adaptations in colonization behavior relevant to microbial biofilm ecology; and (5) object segmentation of complex color images to differentiate target microbes reporting successful cell-cell communication. These unique computational features contribute to the CMEIAS mission of developing accurate and freely accessible tools of image bioinformatics that strengthen microscopy-based approaches for understanding microbial ecology at single-cell resolution.Computation2015-03-0931Review10.3390/computation301007272982079-31972015-03-09doi: 10.3390/computation3010072Frank DazzoBrighid Niccum<![CDATA[Computation, Vol. 3, Pages 58-71: Visual Simulation of Soil-Microbial System Using GPGPU Technology]]>
http://www.mdpi.com/2079-3197/3/1/58
General Purpose (use of) Graphics Processing Units (GPGPU) is a promising technology for simulation upscaling; in particular for bottom–up modelling approaches seeking to translate micro-scale system processes to macro-scale properties. Many existing simulations of soil ecosystems do not recover the emergent system scale properties and this may be a consequence of “missing” information at finer scales. Interpretation of model output can be challenging and we advocate the “built-in” visual simulation afforded by GPGPU implementations. We apply this GPGPU approach to a reaction–diffusion soil ecosystem model with the intent of linking micro (micron) and core (cm) spatial scales to investigate how microbes respond to changing environments and the consequences on soil respiration. The performance is evaluated in terms of computational speed up, spatial upscaling and visual feedback. We conclude that a GPGPU approach can significantly improve computational efficiency and offers the potential added benefit of visual immediacy. For massive spatial domains distribution over GPU devices may still be required.Computation2015-02-2731Article10.3390/computation301005858712079-31972015-02-27doi: 10.3390/computation3010058Ruth FalconerAlasdair Houston<![CDATA[Computation, Vol. 3, Pages 29-57: A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization]]>
http://www.mdpi.com/2079-3197/3/1/29
Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number of atoms involved and the need to simulate over long time periods of biological interest, traditional computational tools, like molecular dynamics, are often infeasible for such systems. Hence, in the current review article, we present and discuss two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction-dominated regime: multiscale perturbation theory and multiscale factorization. These novel analytic foundations provide a self-consistent approach to yield accurate and feasible long-time simulations with atomic detail for a variety of multiscale phenomena, such as viral structural transitions and macromolecular self-assembly. As such, the accuracy and efficiency of the associated algorithms are demonstrated for a few representative biological systems, including satellite tobacco mosaic virus (STMV) and lactoferrin.Computation2015-02-0531Article10.3390/computation301002929572079-31972015-02-05doi: 10.3390/computation3010029Stephen PankavichPeter Ortoleva<![CDATA[Computation, Vol. 3, Pages 2-28: Computational Studies of the Intestinal Host-Microbiota Interactome]]>
http://www.mdpi.com/2079-3197/3/1/2
A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one of the key drivers in the pathophysiology of many of these disorders. This host-microbiota interactome is a set of dynamic and complex processes, and needs to be treated as a distinct entity and subject for study. Disentangling this complex web of interactions will require novel approaches, using a combination of data-driven bioinformatics with knowledge-driven computational modeling. This review describes the computational approaches for investigating the host-microbiota interactome, with emphasis on the human intestinal tract and innate immunity, and highlights open challenges and existing gaps in the computation methodology for advancing our knowledge about this important facet of human health.Computation2015-01-1431Review10.3390/computation30100022282079-31972015-01-14doi: 10.3390/computation3010002Scott ChristleyChase CockrellGary An