Computation, Volume 4, Issue 1 (March 2016) – 15 articles

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. Full article

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 3d_5/2 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. Full article

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. Full article

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 θ_c 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 > θ_c or the occurrence of corner arc menisci at θ < θ_c. 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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article