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Computation, Volume 6, Issue 2 (June 2018)

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Open AccessArticle An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction
Computation 2018, 6(2), 39; https://doi.org/10.3390/computation6020039
Received: 22 April 2018 / Revised: 11 June 2018 / Accepted: 14 June 2018 / Published: 19 June 2018
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Abstract
The energy landscape, which organizes microstates by energies, has shed light on many cellular processes governed by dynamic biological macromolecules leveraging their structural dynamics to regulate interactions with molecular partners. In particular, the protein energy landscape has been central to understanding the relationship
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The energy landscape, which organizes microstates by energies, has shed light on many cellular processes governed by dynamic biological macromolecules leveraging their structural dynamics to regulate interactions with molecular partners. In particular, the protein energy landscape has been central to understanding the relationship between protein structure, dynamics, and function. The landscape view, however, remains underutilized in an important problem in protein modeling, decoy selection in template-free protein structure prediction. Given the amino-acid sequence of a protein, template-free methods compute thousands of structures, known as decoys, as part of an optimization process that seeks minima of an energy function. Selecting biologically-active/native structures from the computed decoys remains challenging. Research has shown that energy is an unreliable indicator of nativeness. In this paper, we advocate that, while comparison of energies is not informative for structures that already populate minima of an energy function, the landscape view exposes the overall organization of generated decoys. As we demonstrate, such organization highlights macrostates that contain native decoys. We present two different computational approaches to extracting such organization and demonstrate through the presented findings that a landscape-driven treatment is promising in furthering research on decoy selection. Full article
(This article belongs to the Special Issue Computation in Molecular Modeling)
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Open AccessArticle An Open-Source Toolbox for PEM Fuel Cell Simulation
Computation 2018, 6(2), 38; https://doi.org/10.3390/computation6020038
Received: 30 March 2018 / Revised: 2 May 2018 / Accepted: 2 May 2018 / Published: 10 May 2018
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Abstract
In this paper, an open-source toolbox that can be used to accurately predict the distribution of the major physical quantities that are transported within a proton exchange membrane (PEM) fuel cell is presented. The toolbox has been developed using the Open Source Field
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In this paper, an open-source toolbox that can be used to accurately predict the distribution of the major physical quantities that are transported within a proton exchange membrane (PEM) fuel cell is presented. The toolbox has been developed using the Open Source Field Operation and Manipulation (OpenFOAM) platform, which is an open-source computational fluid dynamics (CFD) code. The base case results for the distribution of velocity, pressure, chemical species, Nernst potential, current density, and temperature are as expected. The plotted polarization curve was compared to the results from a numerical model and experimental data taken from the literature. The conducted simulations have generated a significant amount of data and information about the transport processes that are involved in the operation of a PEM fuel cell. The key role played by the concentration constant in shaping the cell polarization curve has been explored. The development of the present toolbox is in line with the objectives outlined in the International Energy Agency (IEA, Paris, France) Advanced Fuel Cell Annex 37 that is devoted to developing open-source computational tools to facilitate fuel cell technologies. The work therefore serves as a basis for devising additional features that are not always feasible with a commercial code. Full article
(This article belongs to the Section Computational Engineering)
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Open AccessArticle Modeling the Adaptive Immunity and Both Modes of Transmission in HIV Infection
Computation 2018, 6(2), 37; https://doi.org/10.3390/computation6020037
Received: 15 February 2018 / Revised: 20 April 2018 / Accepted: 4 May 2018 / Published: 8 May 2018
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Abstract
Human immunodeficiency virus (HIV) is a retrovirus that causes HIV infection and over time acquired immunodeficiency syndrome (AIDS). It can be spread and transmitted through two fundamental modes, one by virus-to-cell infection, and the other by direct cell-to-cell transmission. In this paper, we
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Human immunodeficiency virus (HIV) is a retrovirus that causes HIV infection and over time acquired immunodeficiency syndrome (AIDS). It can be spread and transmitted through two fundamental modes, one by virus-to-cell infection, and the other by direct cell-to-cell transmission. In this paper, we propose a new mathematical model that incorporates both modes of transmission and takes into account the role of the adaptive immune response in HIV infection. We first show that the proposed model is mathematically and biologically well posed. Moreover, we prove that the dynamical behavior of the model is fully determined by five threshold parameters. Furthermore, numerical simulations are presented to confirm our theoretical results. Full article
(This article belongs to the Section Computational Biology)
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Open AccessArticle Shannon Entropy in Atoms: A Test for the Assessment of Density Functionals in Kohn-Sham Theory
Computation 2018, 6(2), 36; https://doi.org/10.3390/computation6020036
Received: 10 March 2018 / Revised: 7 April 2018 / Accepted: 22 April 2018 / Published: 3 May 2018
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Abstract
Electron density is used to compute Shannon entropy. The deviation from the Hartree–Fock (HF) of this quantity has been observed to be related to correlation energy. Thus, Shannon entropy is here proposed as a valid quantity to assess the quality of an energy
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Electron density is used to compute Shannon entropy. The deviation from the Hartree–Fock (HF) of this quantity has been observed to be related to correlation energy. Thus, Shannon entropy is here proposed as a valid quantity to assess the quality of an energy density functional developed within Kohn–Sham theory. To this purpose, results from eight different functionals, representative of Jacob’s ladder, are compared with accurate results obtained from diffusion quantum Monte Carlo (DMC) computations. For three series of atomic ions, our results show that the revTPSS and the PBE0 functionals are the best, whereas those based on local density approximation give the largest discrepancy from DMC Shannon entropy. Full article
(This article belongs to the Special Issue In Memory of Walter Kohn—Advances in Density Functional Theory)
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Open AccessArticle Asymptotic Behavior of Exact Exchange for Slabs: Beyond the Leading Order
Computation 2018, 6(2), 35; https://doi.org/10.3390/computation6020035
Received: 26 February 2018 / Revised: 19 April 2018 / Accepted: 21 April 2018 / Published: 29 April 2018
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Abstract
Far outside the surface of slabs, the exact exchange (EXX) potential vx falls off as 1/z , if z denotes the direction perpendicular to the surface and the slab is localized around z=0 . Similarly, the EXX
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Far outside the surface of slabs, the exact exchange (EXX) potential v x falls off as 1 / z , if z denotes the direction perpendicular to the surface and the slab is localized around z = 0 . Similarly, the EXX energy density e x behaves as n / ( 2 z ) , where n is the electron density. Here, an alternative proof of these relations is given, in which the Coulomb singularity in the EXX energy is treated in a particularly careful fashion. This new approach allows the derivation of the next-to-leading order contributions to the asymptotic v x and e x . It turns out that in both cases, the corrections are proportional to 1 / z 2 in general. Full article
(This article belongs to the Special Issue In Memory of Walter Kohn—Advances in Density Functional Theory)
Open AccessArticle Aerodynamic Optimization of Airfoil Profiles for Small Horizontal Axis Wind Turbines
Computation 2018, 6(2), 34; https://doi.org/10.3390/computation6020034
Received: 2 March 2018 / Revised: 19 April 2018 / Accepted: 21 April 2018 / Published: 25 April 2018
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Abstract
The purpose of this study is the development of an automated two-dimensional airfoil shape optimization procedure for small horizontal axis wind turbines (HAWT), with an emphasis on high thrust and aerodynamically stable performance. The procedure combines the Computational Fluid Dynamics (CFD) analysis with
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The purpose of this study is the development of an automated two-dimensional airfoil shape optimization procedure for small horizontal axis wind turbines (HAWT), with an emphasis on high thrust and aerodynamically stable performance. The procedure combines the Computational Fluid Dynamics (CFD) analysis with the Response Surface Methodology (RSM), the Biobjective Mesh Adaptive Direct Search (BiMADS) optimization algorithm and an automatic geometry and mesh generation tool. In CFD analysis, a Reynolds Averaged Numerical Simulation (RANS) is applied in combination with a two-equation turbulence model. For describing the system behaviour under alternating wind conditions, a number of CFD 2D-RANS-Simulations with varying Reynolds numbers and wind angles are performed. The number of cases is reduced by the use of RSM. In the analysis, an emphasis is placed upon the role of the blade-to-blade interaction. The average and the standard deviation of the thrust are optimized by a derivative-free optimization algorithm to define a Pareto optimal set, using the BiMADS algorithm. The results show that improvements in the performance can be achieved by modifications of the blade shape and the present procedure can be used as an effective tool for blade shape optimization. Full article
(This article belongs to the Special Issue Computational Methods in Wind Engineering)
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Open AccessArticle Modeling Confined Cell Migration Mediated by Cytoskeleton Dynamics
Computation 2018, 6(2), 33; https://doi.org/10.3390/computation6020033
Received: 14 February 2018 / Revised: 30 March 2018 / Accepted: 12 April 2018 / Published: 19 April 2018
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Abstract
Cell migration is an important biological process that has generated increasing interest during the last several years. This process is based on three phases: protrusion at the front end of the cell, de-adhesion at the rear end and contraction of the cell body,
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Cell migration is an important biological process that has generated increasing interest during the last several years. This process is based on three phases: protrusion at the front end of the cell, de-adhesion at the rear end and contraction of the cell body, all of them coordinated due to the polymerization/depolymerization of certain cytoskeletal proteins. The aim of this work is to present a mathematical model to simulate the actin polymerization/depolymerization process that regulates the final outcome of cell migration process, considering all the above phases, in a particular case: when the cell is confined in a microfluidic channel. Under these specific conditions, cell migration can be approximated by using one-dimensional simulations. We will propose a system of reaction–diffusion equations to simulate the behavior of the cytoskeletal proteins responsible for protrusion and contraction in the cell, coupled with the mechanical response of the cell, computing its deformations and stresses. Furthermore, a numerical procedure is presented in order to simulate the whole process in a moving and deformable domain corresponding to the cell body. Full article
(This article belongs to the Section Computational Biology)
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Open AccessArticle Wind Pressure Distributions on Buildings Using the Coherent Structure Smagorinsky Model for LES
Computation 2018, 6(2), 32; https://doi.org/10.3390/computation6020032
Received: 22 January 2018 / Revised: 4 April 2018 / Accepted: 10 April 2018 / Published: 14 April 2018
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Abstract
A subgrid-scale model based on coherent structures, called the Coherent Structure Smagorinsky Model (CSM), has been applied to a large eddy simulation to assess its performance in the prediction of wind pressure distributions on buildings. The study cases were carried out for the
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A subgrid-scale model based on coherent structures, called the Coherent Structure Smagorinsky Model (CSM), has been applied to a large eddy simulation to assess its performance in the prediction of wind pressure distributions on buildings. The study cases were carried out for the assessment of an isolated rectangular high-rise building and a building with a setback (both in a uniform flow) and an actual high-rise building in an urban city with turbulent boundary layer flow. For the isolated rectangular high-rise building in uniform flow, the CSM showed good agreement with both the traditional Smagorinsky Model (SM) and the experiments (values within 20%). For the building with a setback as well as the actual high-rise building in an urban city, both of which have a distinctive wind pressure distribution with large negative pressure caused by the complicated flow due to the strong influence of neighboring buildings, the CSM effectively gives more accurate results with less variation than the SM in comparison with the experimental results (within 20%). The CSM also yielded consistent peak pressure coefficients for all wind directions, within 20% of experimental values in a relatively high-pressure region of the case study of the actual high-rise building in an urban city. Full article
(This article belongs to the Special Issue Computational Methods in Wind Engineering)
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Open AccessArticle Application of High-Order Compact Difference Scheme in the Computation of Incompressible Wall-Bounded Turbulent Flows
Computation 2018, 6(2), 31; https://doi.org/10.3390/computation6020031
Received: 6 March 2018 / Revised: 29 March 2018 / Accepted: 4 April 2018 / Published: 11 April 2018
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Abstract
In the present work, a highly efficient incompressible flow solver with a semi-implicit time advancement on a fully staggered grid using a high-order compact difference scheme is developed firstly in the framework of approximate factorization. The fourth-order compact difference scheme is adopted for
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In the present work, a highly efficient incompressible flow solver with a semi-implicit time advancement on a fully staggered grid using a high-order compact difference scheme is developed firstly in the framework of approximate factorization. The fourth-order compact difference scheme is adopted for approximations of derivatives and interpolations in the incompressible Navier–Stokes equations. The pressure Poisson equation is efficiently solved by the fast Fourier transform (FFT). The framework of approximate factorization significantly simplifies the implementation of the semi-implicit time advancing with a high-order compact scheme. Benchmark tests demonstrate the high accuracy of the proposed numerical method. Secondly, by applying the proposed numerical method, we compute turbulent channel flows at low and moderate Reynolds numbers by direct numerical simulation (DNS) and large eddy simulation (LES). It is found that the predictions of turbulence statistics and especially energy spectra can be obviously improved by adopting the high-order scheme rather than the traditional second-order central difference scheme. Full article
(This article belongs to the Section Computational Engineering)
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Open AccessArticle First Principles Study of Topochemical Effects and Electronic Structure Relationships between ANCl and A2N2Se (A = Zr, Ce) Assimilated to Pseudo-Binaries: {AN}Cl and {A2N2}Se
Computation 2018, 6(2), 30; https://doi.org/10.3390/computation6020030
Received: 16 March 2018 / Revised: 22 March 2018 / Accepted: 28 March 2018 / Published: 2 April 2018
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Abstract
Topochemical and electronic structure relationships are shown upon going from ANCl to A2N2Se (A = Zr, Ce) through metathesis. The chalcogen Se (divalent) displacing halogen Cl (monovalent) modifies the arrangements of A–N monolayers within ANCl (…Cl|{AN}|Cl… sequences) to double
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Topochemical and electronic structure relationships are shown upon going from ANCl to A2N2Se (A = Zr, Ce) through metathesis. The chalcogen Se (divalent) displacing halogen Cl (monovalent) modifies the arrangements of A–N monolayers within ANCl (…Cl|{AN}|Cl… sequences) to double layers in A2N2Se (…Se|{A2N2}|Se… sequences). The investigation carried out in the framework of the quantum density functional theory DFT points to peculiar features pertaining to the dominant effect of the A–N covalent bond stronger than ionic A–Cl and ionocovalent A–Se, as identified from analyses of bonding from overlap integral, charge transfer, electron localization function mapping. Electronic density of states shows semi-conducting behavior due to the tetravalent character of A. The resulting overall pseudo-binary compounds are expressed formally with full ionization as {AN}Cl and {A2N2}Se. Full article
(This article belongs to the Special Issue Ab Initio Modelling in Solid State Chemistry)
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Open AccessReview Kohn Anomaly and Phase Stability in Group VB Transition Metals
Computation 2018, 6(2), 29; https://doi.org/10.3390/computation6020029
Received: 28 February 2018 / Revised: 17 March 2018 / Accepted: 21 March 2018 / Published: 26 March 2018
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Abstract
In the periodic table, only a few pure metals exhibit lattice or magnetic instabilities associated with Fermi surface nesting, the classical examples being α-U and Cr. Whereas α-U displays a strong Kohn anomaly in the phonon spectrum that ultimately leads to the formation
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In the periodic table, only a few pure metals exhibit lattice or magnetic instabilities associated with Fermi surface nesting, the classical examples being α-U and Cr. Whereas α-U displays a strong Kohn anomaly in the phonon spectrum that ultimately leads to the formation of charge density waves (CDWs), Cr is known for its nesting-induced spin density waves (SDWs). Recently, it has become clear that a pronounced Kohn anomaly and the corresponding softening in the elastic constants is also the key factor that controls structural transformations and mechanical properties in compressed group VB metals—materials with relatively high superconducting critical temperatures. This article reviews the current understanding of the structural and mechanical behavior of these metals under pressure with an introduction to the concept of the Kohn anomaly and how it is related to the important concept of Peierls instability. We review both experimental and theoretical results showing different manifestations of the Kohn anomaly in the transverse acoustic phonon mode TA (ξ00) in V, Nb, and Ta. Specifically, in V the anomaly triggers a structural transition to a rhombohedral phase, whereas in Nb and Ta it leads to an anomalous reduction in yield strength. Full article
(This article belongs to the Special Issue In Memory of Walter Kohn—Advances in Density Functional Theory)
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Open AccessArticle LES and Wind Tunnel Test of Flow around Two Tall Buildings in Staggered Arrangement
Computation 2018, 6(2), 28; https://doi.org/10.3390/computation6020028
Received: 30 January 2018 / Revised: 19 March 2018 / Accepted: 20 March 2018 / Published: 23 March 2018
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Abstract
Wind flow structures and their consequent wind loads on two high-rise buildings in staggered arrangement are investigated by Large Eddy Simulation (LES). Synchronized pressure and flow field measurements by particle image velocimetry (PIV) are conducted in a boundary layer wind tunnel to validate
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Wind flow structures and their consequent wind loads on two high-rise buildings in staggered arrangement are investigated by Large Eddy Simulation (LES). Synchronized pressure and flow field measurements by particle image velocimetry (PIV) are conducted in a boundary layer wind tunnel to validate the numerical simulations. The instantaneous and time-averaged flow fields are analyzed and discussed in detail. The coherent flow structures in the building gap are clearly observed and the upstream building wake is found to oscillate sideways and meander down to the downstream building in a coherent manner. The disruptive effect on the downstream building wake induced by the upstream building is also observed. Furthermore, the connection between the upstream building wake and the wind loads on the downstream building is explored by the simultaneous data of wind pressures and wind flow fields. Full article
(This article belongs to the Special Issue Computational Methods in Wind Engineering)
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Open AccessArticle Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers
Computation 2018, 6(2), 27; https://doi.org/10.3390/computation6020027
Received: 24 January 2018 / Revised: 26 February 2018 / Accepted: 19 March 2018 / Published: 21 March 2018
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Abstract
In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical
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In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables. Full article
(This article belongs to the Special Issue Computation in Molecular Modeling)
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