Next Issue
Volume 5, March
Previous Issue
Volume 4, September
 
 
From the start of 2016, the journal uses article numbers instead of page numbers to identify articles. If you are required to add page numbers to a citation, you can do with using a colon in the format [article number]:1–[last page], e.g. 10:1–20.

Computation, Volume 4, Issue 4 (December 2016) – 9 articles

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Select all
Export citation of selected articles as:
4121 KiB  
Article
Effect of Pore Structure on Soot Deposition in Diesel Particulate Filter
by Kazuhiro Yamamoto and Tatsuya Sakai
Computation 2016, 4(4), 46; https://doi.org/10.3390/computation4040046 - 02 Dec 2016
Cited by 17 | Viewed by 6730
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 [...] Read more.
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)
Show Figures

Figure 1

684 KiB  
Editorial
Special Issue “50th Anniversary of the Kohn–Sham Theory—Advances in Density Functional Theory”
by Ágnes Nagy and Karlheinz Schwarz
Computation 2016, 4(4), 45; https://doi.org/10.3390/computation4040045 - 22 Nov 2016
Cited by 2 | Viewed by 4080
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 [...] Read more.
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
Show Figures

Figure 1

4991 KiB  
Article
Mathematical Model of a Lithium-Bromide/Water Absorption Refrigeration System Equipped with an Adiabatic Absorber
by Salem M. Osta-Omar and Christopher Micallef
Computation 2016, 4(4), 44; https://doi.org/10.3390/computation4040044 - 17 Nov 2016
Cited by 12 | Viewed by 9280
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, [...] Read more.
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)
Show Figures

Figure 1

1615 KiB  
Article
A Theoretical Study of One- and Two-Photon Activity of D-Luciferin
by Mausumi Chattopadhyaya and Md. Mehboob Alam
Computation 2016, 4(4), 43; https://doi.org/10.3390/computation4040043 - 17 Nov 2016
Cited by 1 | Viewed by 4485
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 [...] Read more.
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
Show Figures

Graphical abstract

2055 KiB  
Article
A Mathematical Spline-Based Model of Cardiac Left Ventricle Anatomy and Morphology
by Sergei Pravdin
Computation 2016, 4(4), 42; https://doi.org/10.3390/computation4040042 - 27 Oct 2016
Cited by 3 | Viewed by 5066
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 [...] Read more.
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)
Show Figures

Figure 1

2344 KiB  
Article
Evaluation of External Memory Access Performance on a High-End FPGA Hybrid Computer
by Konstantinos Kalaitzis, Evripidis Sotiriadis, Ioannis Papaefstathiou and Apostolos Dollas
Computation 2016, 4(4), 41; https://doi.org/10.3390/computation4040041 - 25 Oct 2016
Cited by 52 | Viewed by 3847
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)
Show Figures

Figure 1

4594 KiB  
Article
A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection
by Simeone Marino and Denise E. Kirschner
Computation 2016, 4(4), 39; https://doi.org/10.3390/computation4040039 - 21 Oct 2016
Cited by 32 | Viewed by 8748
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)
Show Figures

Figure 1

1043 KiB  
Editorial
Obituary for Walter Kohn (1923–2016)
by Karlheinz Schwarz, Lu J. Sham, Ann E. Mattsson and Matthias Scheffler
Computation 2016, 4(4), 40; https://doi.org/10.3390/computation4040040 - 20 Oct 2016
Cited by 3 | Viewed by 5455
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
Show Figures

Figure 1

6100 KiB  
Article
Steady-State Anderson Accelerated Coupling of Lattice Boltzmann and Navier–Stokes Solvers
by Atanas Atanasov, Benjamin Uekermann, Carlos A. Pachajoa Mejía, Hans-Joachim Bungartz and Philipp Neumann
Computation 2016, 4(4), 38; https://doi.org/10.3390/computation4040038 - 17 Oct 2016
Cited by 4 | Viewed by 4905
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 [...] Read more.
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)
Show Figures

Figure 1

Previous Issue
Next Issue
Back to TopTop