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Computation, Volume 4, Issue 4 (December 2016)

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Editorial

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Open AccessEditorial Obituary for Walter Kohn (1923–2016)
Computation 2016, 4(4), 40; doi:10.3390/computation4040040
Received: 8 October 2016 / Revised: 13 October 2016 / Accepted: 14 October 2016 / Published: 20 October 2016
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Abstract Walter Kohn (Figure 1) is one of the most cited scientists of our time, who died on 19 April 2016 in Santa Barbara, CA, USA. [...] Full article
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Open AccessEditorial Special Issue “50th Anniversary of the Kohn–Sham Theory—Advances in Density Functional Theory”
Computation 2016, 4(4), 45; doi:10.3390/computation4040045
Received: 15 November 2016 / Revised: 17 November 2016 / Accepted: 17 November 2016 / Published: 22 November 2016
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Abstract
The properties of many materials at the atomic scale depend on the electronic structure, which requires a quantum mechanical treatment. The most widely used approach to make such a treatment feasible is density functional theory (DFT), the advances in which were presented and
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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. Full article
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Research

Jump to: Editorial

Open AccessArticle Evaluation of External Memory Access Performance on a High-End FPGA Hybrid Computer
Computation 2016, 4(4), 41; doi:10.3390/computation4040041
Received: 6 June 2016 / Revised: 9 September 2016 / Accepted: 11 October 2016 / Published: 25 October 2016
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Abstract
The motivation of this research was to evaluate the main memory performance of a hybrid super computer such as the Convey HC-x, and ascertain how the controller performs in several access scenarios, vis-à-vis hand-coded memory prefetches. Such memory patterns are very useful in
[...] Read more.
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. Full article
(This article belongs to the Special Issue High Performance Computing (HPC) Software Design)
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Open AccessArticle A Mathematical Spline-Based Model of Cardiac Left Ventricle Anatomy and Morphology
Computation 2016, 4(4), 42; doi:10.3390/computation4040042
Received: 25 June 2016 / Revised: 19 October 2016 / Accepted: 21 October 2016 / Published: 27 October 2016
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Abstract
Computer simulation of normal and diseased human heart activity requires a 3D anatomical model of the myocardium, including myofibers. For clinical applications, such a model has to be constructed based on routine methods of cardiac visualization, such as sonography. Symmetrical models are shown
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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. Full article
(This article belongs to the Special Issue Multiscale and Hybrid Modeling of the Living Systems)
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Open AccessArticle A Theoretical Study of One- and Two-Photon Activity of D-Luciferin
Computation 2016, 4(4), 43; doi:10.3390/computation4040043
Received: 30 September 2016 / Revised: 8 November 2016 / Accepted: 9 November 2016 / Published: 17 November 2016
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Abstract
In the present work, we have theoretically studied the one and two-photon absorption (OPA and TPA) probabilities of the native D-luciferin molecule and attempted to find the origin of its larger TPA cross-sections in polar solvents than in non-polar ones. The calculations using
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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. Full article
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Open AccessArticle Mathematical Model of a Lithium-Bromide/Water Absorption Refrigeration System Equipped with an Adiabatic Absorber
Computation 2016, 4(4), 44; doi:10.3390/computation4040044
Received: 13 October 2016 / Revised: 3 November 2016 / Accepted: 11 November 2016 / Published: 17 November 2016
Cited by 2 | PDF Full-text (4991 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this paper is to develop a mathematical model for thermodynamic analysis of an absorption refrigeration system equipped with an adiabatic absorber using a lithium-bromide/water (LiBr/water) pair as the working fluid. The working temperature of the generator, adiabatic absorber, condenser, evaporator,
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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. Full article
(This article belongs to the Section Computational Engineering)
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Open AccessArticle Effect of Pore Structure on Soot Deposition in Diesel Particulate Filter
Computation 2016, 4(4), 46; doi:10.3390/computation4040046
Received: 21 October 2016 / Revised: 17 November 2016 / Accepted: 29 November 2016 / Published: 2 December 2016
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Abstract
Nowadays, in the after-treatment of diesel exhaust gas, a diesel particulate filter (DPF) has been used to trap nano-particles of the diesel soot. However, as there are more particles inside the filter, the pressure which corresponds to the filter backpressure increases, which worsens
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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. Full article
(This article belongs to the Special Issue CFD: Recent Advances in Lattice Boltzmann Methods)
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Open AccessArticle Steady-State Anderson Accelerated Coupling of Lattice Boltzmann and Navier–Stokes Solvers
Computation 2016, 4(4), 38; doi:10.3390/computation4040038
Received: 20 July 2016 / Revised: 26 September 2016 / Accepted: 8 October 2016 / Published: 17 October 2016
Cited by 1 | PDF Full-text (6100 KB) | HTML Full-text | XML Full-text
Abstract
We present an Anderson acceleration-based approach to spatially couple three-dimensional Lattice Boltzmann and Navier–Stokes (LBNS) flow simulations. This allows to locally exploit the computational features of both fluid flow solver approaches to the fullest extent and yields enhanced control to match the LB
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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. Full article
(This article belongs to the Special Issue CFD: Recent Advances in Lattice Boltzmann Methods)
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Open AccessFeature PaperArticle A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection
Computation 2016, 4(4), 39; doi:10.3390/computation4040039
Received: 25 August 2016 / Revised: 3 October 2016 / Accepted: 7 October 2016 / Published: 21 October 2016
Cited by 2 | PDF Full-text (4594 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs,
[...] Read more.
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. Full article
(This article belongs to the Special Issue Multiscale and Hybrid Modeling of the Living Systems)
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