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Computation, Volume 9, Issue 4 (April 2021) – 10 articles

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Article
XGRN: Reconstruction of Biological Networks Based on Boosted Trees Regression
Computation 2021, 9(4), 48; https://doi.org/10.3390/computation9040048 - 20 Apr 2021
Viewed by 692
Abstract
In Systems Biology, the complex relationships between different entities in the cells are modeled and analyzed using networks. Towards this aim, a rich variety of gene regulatory network (GRN) inference algorithms has been developed in recent years. However, most algorithms rely solely on [...] Read more.
In Systems Biology, the complex relationships between different entities in the cells are modeled and analyzed using networks. Towards this aim, a rich variety of gene regulatory network (GRN) inference algorithms has been developed in recent years. However, most algorithms rely solely on gene expression data to reconstruct the network. Due to possible expression profile similarity, predictions can contain connections between biologically unrelated genes. Therefore, previously known biological information should also be considered by computational methods to obtain more consistent results, such as experimentally validated interactions between transcription factors and target genes. In this work, we propose XGBoost for gene regulatory networks (XGRN), a supervised algorithm, which combines gene expression data with previously known interactions for GRN inference. The key idea of our method is to train a regression model for each known interaction of the network and then utilize this model to predict new interactions. The regression is performed by XGBoost, a state-of-the-art algorithm using an ensemble of decision trees. In detail, XGRN learns a regression model based on gene expression of the two interactors and then provides predictions using as input the gene expression of other candidate interactors. Application on benchmark datasets and a real large single-cell RNA-Seq experiment resulted in high performance compared to other unsupervised and supervised methods, demonstrating the ability of XGRN to provide reliable predictions. Full article
(This article belongs to the Special Issue Inference of Gene Regulatory Networks Using Randomized Algorithms)
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Article
Non-Hydrostatic Discontinuous/Continuous Galerkin Model for Wave Propagation, Breaking and Runup
Computation 2021, 9(4), 47; https://doi.org/10.3390/computation9040047 - 14 Apr 2021
Cited by 1 | Viewed by 695
Abstract
This paper presents a new depth-integrated non-hydrostatic finite element model for simulating wave propagation, breaking and runup using a combination of discontinuous and continuous Galerkin methods. The formulation decomposes the depth-integrated non-hydrostatic equations into hydrostatic and non-hydrostatic parts. The hydrostatic part is solved [...] Read more.
This paper presents a new depth-integrated non-hydrostatic finite element model for simulating wave propagation, breaking and runup using a combination of discontinuous and continuous Galerkin methods. The formulation decomposes the depth-integrated non-hydrostatic equations into hydrostatic and non-hydrostatic parts. The hydrostatic part is solved with a discontinuous Galerkin finite element method to allow the simulation of discontinuous flows, wave breaking and runup. The non-hydrostatic part led to a Poisson type equation, where the non-hydrostatic pressure is solved using a continuous Galerkin method to allow the modeling of wave propagation and transformation. The model uses linear quadrilateral finite elements for horizontal velocities, water surface elevations and non-hydrostatic pressures approximations. A new slope limiter for quadrilateral elements is developed. The model is verified and validated by a series of analytical solutions and laboratory experiments. Full article
(This article belongs to the Section Computational Engineering)
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Article
Model and Analysis of Economic- and Risk-Based Objective Optimization Problem for Plant Location within Industrial Estates Using Epsilon-Constraint Algorithms
Computation 2021, 9(4), 46; https://doi.org/10.3390/computation9040046 - 14 Apr 2021
Cited by 5 | Viewed by 671
Abstract
In many countries, a number of industrial estates have been established to support the growth of the industrial sector, which is an essential strategy to drive economic growth. Planning for the location of industrial factories within an industrial estate, however, becomes complex, given [...] Read more.
In many countries, a number of industrial estates have been established to support the growth of the industrial sector, which is an essential strategy to drive economic growth. Planning for the location of industrial factories within an industrial estate, however, becomes complex, given the various types of industrial plants and the requirements of utilities to support operations within an industrial park. In this research, we model and analyze bi-objective optimization for locating plants within an industrial estate by considering economic- and risk-based cost objectives. Whereas economic objectives are associated with utility distances between plant locations, risk-based cost is a surrogate criterion derived from safety considerations. Next, risk-based data are further generated from Areal Locations of Hazardous Atmospheres (ALOHA), the hazard modeling program, and solutions to the bi-objective model are obtained from the Epsilon-constraint algorithm. Finally, the model is applied to a regional case study in a Thailand industrial estate, and the Pareto frontier is evaluated to demonstrate the trade-off between objectives. Full article
(This article belongs to the Section Computational Engineering)
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Article
The Influence of Thickness on the Magnetic Properties of Nanocrystalline Thin Films: A Computational Approach
Computation 2021, 9(4), 45; https://doi.org/10.3390/computation9040045 - 12 Apr 2021
Viewed by 572
Abstract
A study of the magnetic behaviour of polycrystalline thin films as a function of their thickness is presented in this work. The grain volume was kept approximately constant in the virtual samples. The model includes the exchange interaction, magneto-crystalline anisotropy, surface anisotropy, boundary [...] Read more.
A study of the magnetic behaviour of polycrystalline thin films as a function of their thickness is presented in this work. The grain volume was kept approximately constant in the virtual samples. The model includes the exchange interaction, magneto-crystalline anisotropy, surface anisotropy, boundary grain anisotropy, dipolar interaction, and Zeeman effect. The thickness-dependence of the critical temperature, blocking temperature, and irreversibility temperature are presented. Surface anisotropy exerts a great influence at very low thicknesses, producing a monodomain regime. As the thickness increases, the dipolar interaction produces a coupling in-plane of single domains per grain which favours superparamagnetic states. At higher thicknesses, the effects of the in-plane anisotropy produced by dipolar interaction and surface anisotropy decrease dramatically. As a result, the superparamagnetic states present three-dimensional local anisotropies by the grain. Full article
(This article belongs to the Section Computational Chemistry)
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Article
Latent Class Model with Heterogeneous Decision Rule for Identification of Factors to the Choice of Drivers’ Seat Belt Use
Computation 2021, 9(4), 44; https://doi.org/10.3390/computation9040044 - 02 Apr 2021
Cited by 1 | Viewed by 628
Abstract
The choice of not buckling a seat belt has resulted in a high number of deaths worldwide. Although extensive studies have been done to identify factors of seat belt use, most of those studies have ignored the presence of heterogeneity across vehicle occupants. [...] Read more.
The choice of not buckling a seat belt has resulted in a high number of deaths worldwide. Although extensive studies have been done to identify factors of seat belt use, most of those studies have ignored the presence of heterogeneity across vehicle occupants. Not accounting for heterogeneity might result in a bias in model outputs. One of the main approaches to capture random heterogeneity is the employment of the latent class (LC) model by means of a discrete distribution. In a standard LC model, the heterogeneity across observations is considered while assuming the homogeneous utility maximization for decision rules. However, that notion ignores the heterogeneity in the decision rule across individual drivers. In other words, while some drivers make a choice of buckling up with some characteristics, others might ignore those factors while making a choice. Those differences could be accommodated for by allowing class allocation to vary based on various socio-economic characteristics and by constraining some of those rules at zeroes across some of the classes. Thus, in this study, in addition to accounting for heterogeneity across individual drivers, we accounted for heterogeneity in the decision rule by varying the parameters for class allocation. Our results showed that the assignment of various observations to classes is a function of factors such as vehicle type, roadway classification, and vehicle license registration. Additionally, the results showed that a minor consideration of the heterogeneous decision rule resulted in a minor gain in model fits, as well as changes in significance and magnitude of the parameter estimates. All of this was despite the challenges of fully identifying exact attributes for class allocation due to the inclusion of high number of attributes. The findings of this study have important implications for the use of an LC model to account for not only the taste heterogeneity but also heterogeneity across the decision rule to enhance model fit and to expand our understanding about the unbiased point estimates of parameters. Full article
Article
Modelling of a Bluff-Body Stabilised Premixed Flames Close to Blow-Off
Computation 2021, 9(4), 43; https://doi.org/10.3390/computation9040043 - 30 Mar 2021
Viewed by 752
Abstract
As emission legislation becomes more stringent, the modelling of turbulent lean premixed combustion is becoming an essential tool for designing efficient and environmentally friendly combustion systems. However, to predict emissions, reliable predictive models are required. Among the promising methods capable of predicting pollutant [...] Read more.
As emission legislation becomes more stringent, the modelling of turbulent lean premixed combustion is becoming an essential tool for designing efficient and environmentally friendly combustion systems. However, to predict emissions, reliable predictive models are required. Among the promising methods capable of predicting pollutant emissions with a long chemical time scale, such as nitrogen oxides (NOx), is conditional moment closure (CMC). However, the practical application of this method to turbulent premixed flames depends on the precision of the conditional scalar dissipation rate,ζ Nc|ζ, model. In this study, an alternative closure for this term is implemented in the RANS-CMC method. The method is validated against the velocity, temperature, and gas composition measurements of lean premixed flames close to blow-off, within the limit of computational fluid dynamic (CFD) capability. Acceptable agreement is achieved between the predicted and measured values near the burner, with an average error of 15%. The model reproduces the flame characteristics; some discrepancies are found within the recirculation region due to significant turbulence intensity. Full article
(This article belongs to the Section Computational Engineering)
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Article
A Shoreline Evolution Model with a Groin Structure under Non-Uniform Breaking Wave Crest Impact
Computation 2021, 9(4), 42; https://doi.org/10.3390/computation9040042 - 26 Mar 2021
Viewed by 756
Abstract
Beach erosion is a natural phenomenon that is not compensated by depositing fresh material on the shoreline while transporting sand away from the shoreline. There are three phenomena that have a serious influence on the coastal structure, such as increases in flooding, accretion, [...] Read more.
Beach erosion is a natural phenomenon that is not compensated by depositing fresh material on the shoreline while transporting sand away from the shoreline. There are three phenomena that have a serious influence on the coastal structure, such as increases in flooding, accretion, and water levels. In addition, the prediction of coastal evolution is used to investigate the topography of the beach. In this research, we present a one-dimensional mathematical model of shoreline evolution, and the parameters that influence this model are described on a monthly basis over a period of one year. Consideration is given to the wave crest impact model for evaluating the impact of the wave crest at that stage. It focuses on the evolution of the shoreline in environments where groins are installed on both sides. The initial and boundary condition setting techniques are proposed by the groins and their environmental parameters. The non-uniform influence of the crest of the breaking wave is so often considered. We then used the traditional forward time centered space technique and the Saulyev finite difference technique to estimate the monthly evolution of the shoreline for each year. Full article
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Article
Electrostatic Circular Membrane MEMS: An Approach to the Optimal Control
Computation 2021, 9(4), 41; https://doi.org/10.3390/computation9040041 - 25 Mar 2021
Cited by 1 | Viewed by 780
Abstract
The recovery of the membrane profile of an electrostatic micro-electro-mechanical system (MEMS) is an important issue, because, when an external electrical voltage is applied, the membrane deforms with the risk of touching the upper plate of the device producing an unwanted electrostatic effect. [...] Read more.
The recovery of the membrane profile of an electrostatic micro-electro-mechanical system (MEMS) is an important issue, because, when an external electrical voltage is applied, the membrane deforms with the risk of touching the upper plate of the device producing an unwanted electrostatic effect. Therefore, it is important to know whether the movement admits stable equilibrium configurations especially when the membrane is closed to the upper plate. In this framework, this work analyzes the behavior of a two-dimensional (2D) electrostatic circular membrane MEMS device subjected to an external voltage. Specifically, starting from a well-known 2D non-linear second-order differential model in which the electrostatic field in the device is proportional to the mean curvature of the membrane, the stability of the only possible equilibrium configuration is studied. Furthermore, when considering that the membrane is equipped with mechanical inertia and that it must not touch the upper plate of the device, a useful range of possible values has been obtained for the applied voltage. Finally, the paper concludes with some computations regarding the variation of potential energy, identifying some optimal control conditions. Full article
(This article belongs to the Section Computational Engineering)
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Article
A Study on Shape-Dependent Settling of Single Particles with Equal Volume Using Surface Resolved Simulations
Computation 2021, 9(4), 40; https://doi.org/10.3390/computation9040040 - 25 Mar 2021
Viewed by 757
Abstract
A detailed knowledge of the influence of a particle’s shape on its settling behavior is useful for the prediction and design of separation processes. Models in the available literature usually fit a given function to experimental data. In this work, a constructive and [...] Read more.
A detailed knowledge of the influence of a particle’s shape on its settling behavior is useful for the prediction and design of separation processes. Models in the available literature usually fit a given function to experimental data. In this work, a constructive and data-driven approach is presented to obtain new drag correlations. To date, the only considered shape parameters are derivatives of the axis lengths and the sphericity. This does not cover all relevant effects, since the process of settling for arbitrarily shaped particles is highly complex. This work extends the list of considered parameters by, e.g., convexity and roundness and evaluates the relevance of each. The aim is to find models describing the drag coefficient and settling velocity, based on this extended set of shape parameters. The data for the investigations are obtained by surface resolved simulations of superellipsoids, applying the homogenized lattice Boltzmann method. To closely study the influence of shape, the particles considered are equal in volume, and therefore cover a range of Reynolds numbers, limited to [9.64, 22.86]. Logistic and polynomial regressions are performed and the quality of the models is investigated with further statistical methods. In addition to the usually studied relation between drag coefficient and Reynolds number, the dependency of the terminal settling velocity on the shape parameters is also investigated. The found models are, with an adjusted coefficient of determination of 0.96 and 0.86, in good agreement with the data, yielding a mean deviation below 5.5% on the training and test dataset. Full article
(This article belongs to the Section Computational Engineering)
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Review
Challenges in the Computational Modeling of the Protein Structure—Activity Relationship
Computation 2021, 9(4), 39; https://doi.org/10.3390/computation9040039 - 24 Mar 2021
Viewed by 768
Abstract
Living organisms are composed of biopolymers (proteins, nucleic acids, carbohydrates and lipid polymers) that are used to keep or transmit information relevant to the state of these organisms at any given time. In these processes, proteins play a central role by displaying different [...] Read more.
Living organisms are composed of biopolymers (proteins, nucleic acids, carbohydrates and lipid polymers) that are used to keep or transmit information relevant to the state of these organisms at any given time. In these processes, proteins play a central role by displaying different activities required to keep or transmit this information. In this review, I present the current knowledge about the protein sequence–structure–activity relationship and the basis for modeling this relationship. Three representative predictors relevant to the modeling of this relationship are summarized to highlight areas that require further improvement and development. I will describe how a basic understanding of this relationship is fundamental in the development of new methods to design proteins, which represents an area of multiple applications in the areas of health and biotechnology. Full article
(This article belongs to the Special Issue Computational Modeling of Structure and Function of Biomolecules)
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