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    - CHEMICAL ENGINEERING (207 journals)
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ENGINEERING (1267 journals)                  1 2 3 4 5 6 7 | Last

Showing 1 - 200 of 1205 Journals sorted alphabetically
3 Biotech     Open Access   (Followers: 8)
3D Research     Hybrid Journal   (Followers: 21)
AAPG Bulletin     Hybrid Journal   (Followers: 8)
AASRI Procedia     Open Access   (Followers: 14)
Abstract and Applied Analysis     Open Access   (Followers: 3)
Aceh International Journal of Science and Technology     Open Access   (Followers: 2)
ACS Nano     Full-text available via subscription   (Followers: 273)
Acta Geotechnica     Hybrid Journal   (Followers: 7)
Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 7)
Acta Polytechnica : Journal of Advanced Engineering     Open Access   (Followers: 3)
Acta Scientiarum. Technology     Open Access   (Followers: 3)
Acta Universitatis Cibiniensis. Technical Series     Open Access  
Active and Passive Electronic Components     Open Access   (Followers: 7)
Adaptive Behavior     Hybrid Journal   (Followers: 11)
Adıyaman Üniversitesi Mühendislik Bilimleri Dergisi     Open Access  
Adsorption     Hybrid Journal   (Followers: 4)
Advanced Engineering Forum     Full-text available via subscription   (Followers: 7)
Advanced Journal of Graduate Research     Open Access  
Advanced Science     Open Access   (Followers: 5)
Advanced Science Focus     Free   (Followers: 5)
Advanced Science Letters     Full-text available via subscription   (Followers: 10)
Advanced Science, Engineering and Medicine     Partially Free   (Followers: 7)
Advanced Synthesis & Catalysis     Hybrid Journal   (Followers: 18)
Advances in Calculus of Variations     Hybrid Journal   (Followers: 2)
Advances in Catalysis     Full-text available via subscription   (Followers: 5)
Advances in Complex Systems     Hybrid Journal   (Followers: 7)
Advances in Engineering Software     Hybrid Journal   (Followers: 27)
Advances in Fuel Cells     Full-text available via subscription   (Followers: 17)
Advances in Fuzzy Systems     Open Access   (Followers: 5)
Advances in Geosciences (ADGEO)     Open Access   (Followers: 13)
Advances in Heat Transfer     Full-text available via subscription   (Followers: 21)
Advances in Human Factors/Ergonomics     Full-text available via subscription   (Followers: 22)
Advances in Magnetic and Optical Resonance     Full-text available via subscription   (Followers: 9)
Advances in Natural Sciences: Nanoscience and Nanotechnology     Open Access   (Followers: 29)
Advances in Operations Research     Open Access   (Followers: 12)
Advances in OptoElectronics     Open Access   (Followers: 6)
Advances in Physics Theories and Applications     Open Access   (Followers: 13)
Advances in Polymer Science     Hybrid Journal   (Followers: 43)
Advances in Porous Media     Full-text available via subscription   (Followers: 5)
Advances in Remote Sensing     Open Access   (Followers: 44)
Advances in Science and Research (ASR)     Open Access   (Followers: 6)
Aerobiologia     Hybrid Journal   (Followers: 3)
African Journal of Science, Technology, Innovation and Development     Hybrid Journal   (Followers: 6)
AIChE Journal     Hybrid Journal   (Followers: 35)
Ain Shams Engineering Journal     Open Access   (Followers: 5)
Akademik Platform Mühendislik ve Fen Bilimleri Dergisi     Open Access   (Followers: 1)
Alexandria Engineering Journal     Open Access   (Followers: 1)
AMB Express     Open Access   (Followers: 1)
American Journal of Applied Sciences     Open Access   (Followers: 26)
American Journal of Engineering and Applied Sciences     Open Access   (Followers: 10)
American Journal of Engineering Education     Open Access   (Followers: 9)
American Journal of Environmental Engineering     Open Access   (Followers: 16)
American Journal of Industrial and Business Management     Open Access   (Followers: 24)
Analele Universitatii Ovidius Constanta - Seria Chimie     Open Access  
Annals of Combinatorics     Hybrid Journal   (Followers: 4)
Annals of Pure and Applied Logic     Open Access   (Followers: 2)
Annals of Regional Science     Hybrid Journal   (Followers: 7)
Annals of Science     Hybrid Journal   (Followers: 7)
Antarctic Science     Hybrid Journal   (Followers: 1)
Applicable Algebra in Engineering, Communication and Computing     Hybrid Journal   (Followers: 2)
Applicable Analysis: An International Journal     Hybrid Journal   (Followers: 1)
Applied Catalysis A: General     Hybrid Journal   (Followers: 6)
Applied Catalysis B: Environmental     Hybrid Journal   (Followers: 18)
Applied Clay Science     Hybrid Journal   (Followers: 6)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 11)
Applied Magnetic Resonance     Hybrid Journal   (Followers: 4)
Applied Nanoscience     Open Access   (Followers: 8)
Applied Network Science     Open Access   (Followers: 3)
Applied Numerical Mathematics     Hybrid Journal   (Followers: 5)
Applied Physics Research     Open Access   (Followers: 5)
Applied Sciences     Open Access   (Followers: 3)
Applied Spatial Analysis and Policy     Hybrid Journal   (Followers: 4)
Arabian Journal for Science and Engineering     Hybrid Journal   (Followers: 5)
Archives of Computational Methods in Engineering     Hybrid Journal   (Followers: 5)
Archives of Foundry Engineering     Open Access  
Archives of Thermodynamics     Open Access   (Followers: 8)
Arkiv för Matematik     Hybrid Journal   (Followers: 1)
ASEE Prism     Full-text available via subscription   (Followers: 3)
Asia-Pacific Journal of Science and Technology     Open Access  
Asian Engineering Review     Open Access  
Asian Journal of Applied Science and Engineering     Open Access   (Followers: 1)
Asian Journal of Applied Sciences     Open Access   (Followers: 2)
Asian Journal of Biotechnology     Open Access   (Followers: 8)
Asian Journal of Control     Hybrid Journal  
Asian Journal of Current Engineering & Maths     Open Access  
Asian Journal of Technology Innovation     Hybrid Journal   (Followers: 8)
Assembly Automation     Hybrid Journal   (Followers: 2)
at - Automatisierungstechnik     Hybrid Journal   (Followers: 1)
ATZagenda     Hybrid Journal  
ATZextra worldwide     Hybrid Journal  
Australasian Physical & Engineering Sciences in Medicine     Hybrid Journal   (Followers: 1)
Australian Journal of Multi-Disciplinary Engineering     Full-text available via subscription   (Followers: 2)
Autonomous Mental Development, IEEE Transactions on     Hybrid Journal   (Followers: 9)
Avances en Ciencias e Ingeniería     Open Access  
Balkan Region Conference on Engineering and Business Education     Open Access   (Followers: 1)
Bangladesh Journal of Scientific and Industrial Research     Open Access  
Basin Research     Hybrid Journal   (Followers: 5)
Batteries     Open Access   (Followers: 6)
Bautechnik     Hybrid Journal   (Followers: 1)
Bell Labs Technical Journal     Hybrid Journal   (Followers: 28)
Beni-Suef University Journal of Basic and Applied Sciences     Open Access   (Followers: 4)
BER : Manufacturing Survey : Full Survey     Full-text available via subscription   (Followers: 1)
BER : Motor Trade Survey     Full-text available via subscription  
BER : Retail Sector Survey     Full-text available via subscription   (Followers: 1)
BER : Retail Survey : Full Survey     Full-text available via subscription   (Followers: 1)
BER : Survey of Business Conditions in Manufacturing : An Executive Summary     Full-text available via subscription   (Followers: 3)
BER : Survey of Business Conditions in Retail : An Executive Summary     Full-text available via subscription   (Followers: 3)
Beyond : Undergraduate Research Journal     Open Access  
Bhakti Persada : Jurnal Aplikasi IPTEKS     Open Access  
Bharatiya Vaigyanik evam Audyogik Anusandhan Patrika (BVAAP)     Open Access   (Followers: 1)
Bilge International Journal of Science and Technology Research     Open Access  
Biofuels Engineering     Open Access   (Followers: 1)
Biointerphases     Open Access   (Followers: 1)
Biomaterials Science     Full-text available via subscription   (Followers: 11)
Biomedical Engineering     Hybrid Journal   (Followers: 15)
Biomedical Engineering and Computational Biology     Open Access   (Followers: 13)
Biomedical Engineering Letters     Hybrid Journal   (Followers: 5)
Biomedical Engineering, IEEE Reviews in     Full-text available via subscription   (Followers: 21)
Biomedical Engineering, IEEE Transactions on     Hybrid Journal   (Followers: 37)
Biomedical Engineering: Applications, Basis and Communications     Hybrid Journal   (Followers: 5)
Biomedical Microdevices     Hybrid Journal   (Followers: 9)
Biomedical Science and Engineering     Open Access   (Followers: 4)
Biomedizinische Technik - Biomedical Engineering     Hybrid Journal   (Followers: 1)
Biomicrofluidics     Open Access   (Followers: 4)
BioNanoMaterials     Hybrid Journal   (Followers: 2)
Biotechnology Progress     Hybrid Journal   (Followers: 39)
Bitlis Eren University Journal of Science and Technology     Open Access  
Boletin Cientifico Tecnico INIMET     Open Access  
Botswana Journal of Technology     Full-text available via subscription   (Followers: 1)
Boundary Value Problems     Open Access   (Followers: 1)
Brazilian Journal of Science and Technology     Open Access   (Followers: 2)
Broadcasting, IEEE Transactions on     Hybrid Journal   (Followers: 12)
Bulletin of Canadian Petroleum Geology     Full-text available via subscription   (Followers: 13)
Bulletin of Engineering Geology and the Environment     Hybrid Journal   (Followers: 14)
Bulletin of the Crimean Astrophysical Observatory     Hybrid Journal  
Cahiers, Droit, Sciences et Technologies     Open Access  
Calphad     Hybrid Journal   (Followers: 2)
Canadian Geotechnical Journal     Hybrid Journal   (Followers: 31)
Canadian Journal of Remote Sensing     Full-text available via subscription   (Followers: 42)
Case Studies in Engineering Failure Analysis     Open Access   (Followers: 6)
Case Studies in Thermal Engineering     Open Access   (Followers: 5)
Catalysis Communications     Hybrid Journal   (Followers: 6)
Catalysis Letters     Hybrid Journal   (Followers: 2)
Catalysis Reviews: Science and Engineering     Hybrid Journal   (Followers: 7)
Catalysis Science and Technology     Free   (Followers: 8)
Catalysis Surveys from Asia     Hybrid Journal   (Followers: 3)
Catalysis Today     Hybrid Journal   (Followers: 7)
CEAS Space Journal     Hybrid Journal   (Followers: 2)
Cellular and Molecular Neurobiology     Hybrid Journal   (Followers: 3)
Central European Journal of Engineering     Hybrid Journal  
Chaos : An Interdisciplinary Journal of Nonlinear Science     Hybrid Journal   (Followers: 2)
Chaos, Solitons & Fractals     Hybrid Journal   (Followers: 3)
Chinese Journal of Catalysis     Full-text available via subscription   (Followers: 2)
Chinese Journal of Engineering     Open Access   (Followers: 2)
Chinese Science Bulletin     Open Access   (Followers: 1)
Ciencia e Ingenieria Neogranadina     Open Access  
Ciencia en su PC     Open Access   (Followers: 1)
Ciencias Holguin     Open Access   (Followers: 3)
CienciaUAT     Open Access   (Followers: 1)
Cientifica     Open Access  
CIRP Annals - Manufacturing Technology     Full-text available via subscription   (Followers: 11)
CIRP Journal of Manufacturing Science and Technology     Full-text available via subscription   (Followers: 13)
City, Culture and Society     Hybrid Journal   (Followers: 21)
Clay Minerals     Full-text available via subscription   (Followers: 10)
Clean Air Journal     Full-text available via subscription   (Followers: 1)
Clinical Science     Full-text available via subscription   (Followers: 9)
Coal Science and Technology     Full-text available via subscription   (Followers: 3)
Coastal Engineering     Hybrid Journal   (Followers: 11)
Coastal Engineering Journal     Hybrid Journal   (Followers: 6)
Coatings     Open Access   (Followers: 4)
Cogent Engineering     Open Access   (Followers: 2)
Cognitive Computation     Hybrid Journal   (Followers: 4)
Color Research & Application     Hybrid Journal   (Followers: 2)
COMBINATORICA     Hybrid Journal  
Combustion Theory and Modelling     Hybrid Journal   (Followers: 14)
Combustion, Explosion, and Shock Waves     Hybrid Journal   (Followers: 14)
Communications Engineer     Hybrid Journal   (Followers: 1)
Communications in Numerical Methods in Engineering     Hybrid Journal   (Followers: 2)
Components, Packaging and Manufacturing Technology, IEEE Transactions on     Hybrid Journal   (Followers: 28)
Composite Interfaces     Hybrid Journal   (Followers: 7)
Composite Structures     Hybrid Journal   (Followers: 277)
Composites Part A : Applied Science and Manufacturing     Hybrid Journal   (Followers: 208)
Composites Part B : Engineering     Hybrid Journal   (Followers: 249)
Composites Science and Technology     Hybrid Journal   (Followers: 193)
Comptes Rendus Mécanique     Full-text available via subscription   (Followers: 2)
Computation     Open Access   (Followers: 1)
Computational Geosciences     Hybrid Journal   (Followers: 16)
Computational Optimization and Applications     Hybrid Journal   (Followers: 7)
Computational Science and Discovery     Full-text available via subscription   (Followers: 2)
Computer Applications in Engineering Education     Hybrid Journal   (Followers: 8)
Computer Science and Engineering     Open Access   (Followers: 19)
Computers & Geosciences     Hybrid Journal   (Followers: 31)
Computers & Mathematics with Applications     Full-text available via subscription   (Followers: 8)
Computers and Electronics in Agriculture     Hybrid Journal   (Followers: 5)
Computers and Geotechnics     Hybrid Journal   (Followers: 11)
Computing and Visualization in Science     Hybrid Journal   (Followers: 7)
Computing in Science & Engineering     Full-text available via subscription   (Followers: 33)
Conciencia Tecnologica     Open Access  
Concurrent Engineering     Hybrid Journal   (Followers: 3)
Continuum Mechanics and Thermodynamics     Hybrid Journal   (Followers: 8)

        1 2 3 4 5 6 7 | Last

Journal Cover
Number of Followers: 1  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2079-3197
Published by MDPI Homepage  [202 journals]
  • Computation, Vol. 6, Pages 27: Testing Convergence of Different
           Free-Energy Methods in a Simple Analytical System with Hidden Barriers

    • Authors: S. Paz, Cameron Abrams
      First page: 27
      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 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.
      Citation: Computation
      PubDate: 2018-03-21
      DOI: 10.3390/computation6020027
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 28: LES and Wind Tunnel Test of Flow around Two
           Tall Buildings in Staggered Arrangement

    • Authors: Gongbo Zu, Kit Lam
      First page: 28
      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 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.
      Citation: Computation
      PubDate: 2018-03-23
      DOI: 10.3390/computation6020028
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 29: Kohn Anomaly and Phase Stability in Group
           VB Transition Metals

    • Authors: Alexander Landa, Per Söderlind, Ivan Naumov, John Klepeis, Levente Vitos
      First page: 29
      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 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.
      Citation: Computation
      PubDate: 2018-03-26
      DOI: 10.3390/computation6020029
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 30: 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

    • Authors: Samir Matar
      First page: 30
      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 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.
      Citation: Computation
      PubDate: 2018-04-02
      DOI: 10.3390/computation6020030
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 31: Application of High-Order Compact
           Difference Scheme in the Computation of Incompressible Wall-Bounded
           Turbulent Flows

    • Authors: Ruifeng Hu, Limin Wang, Ping Wang, Yan Wang, Xiaojing Zheng
      First page: 31
      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 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.
      Citation: Computation
      PubDate: 2018-04-11
      DOI: 10.3390/computation6020031
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 32: Wind Pressure Distributions on Buildings
           Using the Coherent Structure Smagorinsky Model for LES

    • Authors: Pham Phuc, Tsuyoshi Nozu, Hirotoshi Kikuchi, Kazuki Hibi, Yukio Tamura
      First page: 32
      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 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.
      Citation: Computation
      PubDate: 2018-04-14
      DOI: 10.3390/computation6020032
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 33: Modeling Confined Cell Migration Mediated
           by Cytoskeleton Dynamics

    • Authors: María Teresa Sánchez, José Manuel García-Aznar
      First page: 33
      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, 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.
      Citation: Computation
      PubDate: 2018-04-19
      DOI: 10.3390/computation6020033
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 34: Aerodynamic Optimization of Airfoil
           Profiles for Small Horizontal Axis Wind Turbines

    • Authors: Ali Cemal Benim, Michael Diederich, Björn Pfeiffelmann
      First page: 34
      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 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.
      Citation: Computation
      PubDate: 2018-04-25
      DOI: 10.3390/computation6020034
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 35: Asymptotic Behavior of Exact Exchange for
           Slabs: Beyond the Leading Order

    • Authors: Eberhard Engel
      First page: 35
      Abstract: 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.
      Citation: Computation
      PubDate: 2018-04-29
      DOI: 10.3390/computation6020035
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 36: Shannon Entropy in Atoms: A Test for the
           Assessment of Density Functionals in Kohn-Sham Theory

    • Authors: Claudio Amovilli, Franca Floris
      First page: 36
      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 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.
      Citation: Computation
      PubDate: 2018-05-03
      DOI: 10.3390/computation6020036
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 37: Modeling the Adaptive Immunity and Both
           Modes of Transmission in HIV Infection

    • Authors: Khalid Hattaf, Noura Yousfi
      First page: 37
      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 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.
      Citation: Computation
      PubDate: 2018-05-08
      DOI: 10.3390/computation6020037
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 38: An Open-Source Toolbox for PEM Fuel Cell

    • Authors: Jean-Paul Kone, Xinyu Zhang, Yuying Yan, Stephen Adegbite
      First page: 38
      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 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.
      Citation: Computation
      PubDate: 2018-05-10
      DOI: 10.3390/computation6020038
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 39: An Energy Landscape Treatment of Decoy
           Selection in Template-Free Protein Structure Prediction

    • Authors: Nasrin Akhter, Wanli Qiao, Amarda Shehu
      First page: 39
      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 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.
      Citation: Computation
      PubDate: 2018-06-19
      DOI: 10.3390/computation6020039
      Issue No: Vol. 6, No. 2 (2018)
  • Computation, Vol. 6, Pages 2: Temporal Variation of the Pressure from a
           Steady Impinging Jet Model of Dry Microburst-Like Wind Using URANS

    • Authors: Martin Skote, Tze Sim, Narasimalu Srikanth
      First page: 2
      Abstract: The objective of this study is to investigate the temporal behavior of the pressure field of a stationary dry microburst-like wind phenomenon utilizing Unsteady Reynolds-averaged Navier-Stokes (URANS) numerical simulations. Using an axisymmetric steady impinging jet model, the dry microburst-like wind is simulated from the initial release of a steady downdraft flow, till the time after the primary vortices have fully convected out of the stagnation region. The validated URANS results presented herein shed light on the temporal variation of the pressure field which is in agreement with the qualitative description obtained from field measurements. The results have an impact on understanding the wind load on structures from the initial touch-down phase of the downdraft from a microburst. The investigation is based on CFD techniques, together with a simple impinging jet model that does not include any microphysical processes. Unlike previous investigations, this study focuses on the transient pressure field from a downdraft without obstacles.
      Citation: Computation
      PubDate: 2018-01-05
      DOI: 10.3390/computation6010002
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 3: Molecular Dynamics Simulation of High
           Density DNA Arrays

    • Authors: Rudolf Podgornik, Julija Zavadlav, Matej Praprotnik
      First page: 3
      Abstract: Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.
      Citation: Computation
      PubDate: 2018-01-08
      DOI: 10.3390/computation6010003
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 4: Acknowledgement to Reviewers of Computation
           in 2017

    • Authors: Computation Editorial Office
      First page: 4
      Abstract: Peer review is an essential part in the publication process, ensuring that Computation maintains high quality standards for its published papers.
      Citation: Computation
      PubDate: 2018-01-17
      DOI: 10.3390/computation6010004
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 5: Optimization of Airfoils Using the Adjoint
           Approach and the Influence of Adjoint Turbulent Viscosity

    • Authors: Matthias Schramm, Bernhard Stoevesandt, Joachim Peinke
      First page: 5
      Abstract: The adjoint approach in gradient-based optimization combined with computational fluid dynamics is commonly applied in various engineering fields. In this work, the gradients are used for the design of a two-dimensional airfoil shape, where the aim is a change in lift and drag coefficient, respectively, to a given target value. The optimizations use the unconstrained quasi-Newton method with an approximation of the Hessian. The flow field is computed with a finite-volume solver where the continuous adjoint approach is implemented. A common assumption in this approach is the use of the same turbulent viscosity in the adjoint diffusion term as for the primal flow field. The effect of this so-called “frozen turbulence” assumption is compared to the results using adjoints to the Spalart–Allmaras turbulence model. The comparison is done at a Reynolds number of R e = 2 × 10 6 for two different airfoils at different angles of attack.
      Citation: Computation
      PubDate: 2018-01-20
      DOI: 10.3390/computation6010005
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 6: Implementation and Validation of
           Semi-Implicit WENO Schemes Using OpenFOAM®

    • Authors: Tobias Martin, Ivan Shevchuk
      First page: 6
      Abstract: In this article, the development of high-order semi-implicit interpolation schemes for convection terms on unstructured grids is presented. It is based on weighted essentially non-oscillatory (WENO) reconstructions which can be applied to the evaluation of any field in finite volumes using its known cell-averaged values. Here, the algorithm handles convex cells in arbitrary three-dimensional meshes. The implementation is parallelized using the Message Passing Interface. All schemes are embedded in the code structure of OpenFOAM® resulting in the access to a huge open-source community and the applicability to high-level programming. Several verification cases and applications of the scalar advection equation and the incompressible Navier-Stokes equations show the improved accuracy of the WENO approach due to a mapping of the stencil to a reference space without scaling effects. An efficiency analysis indicates an increased computational effort of high-order schemes in comparison to available high-resolution methods. However, the reconstruction time can be efficiently decreased when more processors are used.
      Citation: Computation
      PubDate: 2018-01-24
      DOI: 10.3390/computation6010006
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 7: Solid-State Testing of a
           Van-Der-Waals-Corrected Exchange-Correlation Functional Based on the
           Semiclassical Atom Theory

    • Authors: Aleksandr Terentjev, Pietro Cortona, Lucian Constantin, José Pitarke, Fabio Della Sala, Eduardo Fabiano
      First page: 7
      Abstract: We extend the SG4 generalized gradient approximation, developed for covalent and ionic solids with a nonlocal van der Waals functional. The resulting SG4-rVV10m functional is tested, considering two possible parameterizations, for various kinds of bulk solids including layered materials and molecular crystals as well as regular bulk materials. The results are compared to those of similar methods, PBE + rVV10L and rVV10. In most cases, SG4-rVV10m yields a quite good description of systems (from iono-covalent to hydrogen-bond and dispersion interactions), being competitive with PBE + rVV10L and rVV10 for dispersion-dominated systems and slightly superior for iono-covalent ones. Thus, it shows a promising applicability for solid-state applications. In a few cases, however, overbinding is observed. This is analysed in terms of gradient contributions to the functional.
      Citation: Computation
      PubDate: 2018-01-25
      DOI: 10.3390/computation6010007
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 8: 3D FEM Analysis of a Pile-Supported Riverine
           Platform under Environmental Loads Incorporating Soil-Pile Interaction

    • Authors: Denise-Penelope Kontoni, Ahmed Farghaly
      First page: 8
      Abstract: An existing riverine platform in Egypt, together with its pile group foundation, is analyzed under environmental loads using 3D FEM structural analysis software incorporating soil-pile interaction. The interaction between the transfer plate and the piles supporting the platform is investigated. Two connection conditions were studied assuming fixed or hinged connection between the piles and the reinforced concrete platform for the purpose of comparison of the structural behavior. The analysis showed that the fixed or hinged connection condition between the piles and the platform altered the values and distribution of displacements, normal force, bending moments, and shear forces along the length of each pile. The distribution of piles in the pile group affects the stress distribution on both the soil and platform. The piles were found to suffer from displacement failure rather than force failure. Moreover, the resulting bending stresses on the reinforced concrete plate in the case of a fixed connection between the piles and the platform were almost doubled and much higher than the allowable reinforced concrete stress and even exceeded the ultimate design strength and thus the environmental loads acting on a pile-supported riverine offshore platform may cause collapse if they are not properly considered in the structural analysis and design.
      Citation: Computation
      PubDate: 2018-01-25
      DOI: 10.3390/computation6010008
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 9: An Overview of Network-Based and -Free
           Approaches for Stochastic Simulation of Biochemical Systems

    • Authors: Abhishekh Gupta, Pedro Mendes
      First page: 9
      Abstract: Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into two categories: network-based and -free simulation. The network-based approach requires that the full network of reactions be established at the start, while the network-free approach is based on reaction rules that encode classes of reactions, and by applying rule transformations, it generates reaction events as they are needed without ever having to derive the entire network. In this study, we compare the efficiency and limitations of several available implementations of these two approaches. The results allow for an informed selection of the implementation and methodology for specific biochemical modeling applications.
      Citation: Computation
      PubDate: 2018-01-31
      DOI: 10.3390/computation6010009
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 10: Seismic Response of Adjacent Unequal
           Buildings Subjected to Double Pounding Considering Soil-Structure

    • Authors: Denise-Penelope Kontoni, Ahmed Farghaly
      First page: 10
      Abstract: Various cases of two adjacent multi-story buildings with different numbers of floors and equal or unequal foundation levels under earthquake loading and considering soil-structure interaction (SSI) are investigated. A two-dimensional model for each case of the two adjacent unequal buildings without separation distance is used and a special arrangement of contact elements in the contact zone is employed to fulfil all possible deformation contact modes which take place under seismic loading. The soil is modelled by two-dimensional 4-node elements which are in contact with the foundations of the two adjacent buildings. This paper studies the earthquake-induced double pounding that takes place between the two adjacent unequal height buildings in some upper points at superstructure in the contact zone and also at foundation level, considering soil-structure interaction (SSI). The double pounding and the soil-structure interaction (SSI) effects should be taken into consideration in the seismic analysis of adjacent buildings especially those with different heights and different foundation levels.
      Citation: Computation
      PubDate: 2018-02-01
      DOI: 10.3390/computation6010010
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 11: Holonomic Constraints: A Case for
           Statistical Mechanics of Non-Hamiltonian Systems

    • Authors: Giovanni Ciccotti, Mauro Ferrario
      First page: 11
      Abstract: A dynamical system submitted to holonomic constraints is Hamiltonian only if considered in the reduced phase space of its generalized coordinates and momenta, which need to be defined ad hoc in each particular case. However, specially in molecular simulations, where the number of degrees of freedom is exceedingly high, the representation in generalized coordinates is completely unsuitable, although conceptually unavoidable, to provide a rigorous description of its evolution and statistical properties. In this paper, we first review the state of the art of the numerical approach that defines the way to conserve exactly the constraint conditions (by an algorithm universally known as SHAKE) and permits integrating the equations of motion directly in the phase space of the natural Cartesian coordinates and momenta of the system. We then discuss in detail SHAKE numerical implementations in the notable cases of Verlet and velocity-Verlet algorithms. After discussing in the same framework how constraints modify the properties of the equilibrium ensemble, we show how, at the price of moving to a dynamical system no more (directly) Hamiltonian, it is possible to provide a direct interpretation of the dynamical system and so derive its Statistical Mechanics both at equilibrium and in non-equilibrium conditions. To achieve that, we generalize the statistical treatment to systems no longer conserving the phase space volume (equivalently, we introduce a non-Euclidean invariant measure in phase space) and derive a generalized Liouville equation describing the ensemble even out of equilibrium. As a result, we can extend the response theory of Kubo (linear and nonlinear) to systems subjected to constraints.
      Citation: Computation
      PubDate: 2018-02-01
      DOI: 10.3390/computation6010011
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 12: A Microwave Reflectometry Technique for
           Profiling the Dielectric-Conductivity Properties of the Hagia Sophia Globe

    • Authors: Christos Vazouras, George Kasapoglu, Evangelia Karagianni, Nikolaos Uzunoglu
      First page: 12
      Abstract: A microwave free space reflectometry technique with swept frequency measurements for the profiling of wall structures and the detection of hidden (covered) layers has been applied to the Hagia Sophia byzantine monument. Experimental measurement results are presented and compared with three-dimensional (3D) simulated results, exhibiting fair agreement in some (though not all) aspects. Based on the experimental results, the possibility of clear discrimination between regions with and without covered mosaic layers, and hence the detection of such layers, is demonstrated.
      Citation: Computation
      PubDate: 2018-02-02
      DOI: 10.3390/computation6010012
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 13: Assessing Density-Functional Theory for

    • Authors: Per Söderlind, David Young
      First page: 13
      Abstract: The last decade has seen a continued development of better experimental techniques to measure equation-of-state (EOS) for various materials. These improvements of both static and shock-compression approaches have increased the accuracy of the EOS and challenged the complimentary theoretical modeling. The conventional modeling of EOS, at least at pressure and temperature conditions that are not too extreme, is founded on density-functional theory (DFT). Naturally, there is an increased interest in the accuracy of DFT as the measurements are becoming more refined and there is a particular interest in the robustness and validity of DFT at conditions where experimental data are not available. Here, we consider a broad and large set of 64 elemental solids from low atomic number Z up to the very high Z actinide metals. The intent is to compare DFT with experimental zero-temperature isotherms up to 1 Mbar (100 GPa) and draw conclusions regarding the theoretical (DFT) error and quantify a reasonable and defensible approach to define the theoretical uncertainty. We find that in all 64 cases the DFT error at high pressure is smaller than or equal to the DFT error at lower pressures which thus provides an upper bound to the error at high compression.
      Citation: Computation
      PubDate: 2018-02-03
      DOI: 10.3390/computation6010013
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 14: Analysis, Synchronization and Circuit
           Design of a 4D Hyperchaotic Hyperjerk System

    • Authors: Petros Daltzis, Christos Volos, Hector Nistazakis, Andreas Tsigopoulos, George Tombras
      First page: 14
      Abstract: In this work, a 4D hyperchaotic hyperjerk system, with better results for its Lyapunov exponents and Kaplan–Yorke dimension regarding other systems of this family, as well as its circuit implementation, is presented. Hyperchaotic hyperjerk systems depict complex dynamical behavior in a high-dimensional phase space with n ≥ 4, offering robustness against many types of attacks in private communications. For this reason, an adaptive controller in order to achieve global chaos synchronization of coupled 4D hyperchaotic hyperjerk systems with unknown parameters is designed. The adaptive results in this work are proved using Lyapunov stability theory and the effectiveness of the proposed synchronization scheme is confirmed through the simulation results.
      Citation: Computation
      PubDate: 2018-02-06
      DOI: 10.3390/computation6010014
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 15: Using the Maximum Entropy Principle to
           Combine Simulations and Solution Experiments

    • Authors: Andrea Cesari, Sabine Reißer, Giovanni Bussi
      First page: 15
      Abstract: Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becoming common to integrate MD simulations with experimental data obtained from ensemble measurements. We review here the approaches that can be used to combine MD and experiment under the guidance of the maximum entropy principle. We mostly focus on methods based on Lagrangian multipliers, either implemented as reweighting of existing simulations or through an on-the-fly optimization. We discuss how errors in the experimental data can be modeled and accounted for. Finally, we use simple model systems to illustrate the typical difficulties arising when applying these methods.
      Citation: Computation
      PubDate: 2018-02-06
      DOI: 10.3390/computation6010015
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 16: Simulation and Optimization of Control of
           Selected Phases of Gyroplane Flight

    • Authors: Wienczyslaw Stalewski
      First page: 16
      Abstract: Optimization methods are increasingly used to solve problems in aeronautical engineering. Typically, optimization methods are utilized in the design of an aircraft airframe or its structure. The presented study is focused on improvement of aircraft flight control procedures through numerical optimization. The optimization problems concern selected phases of flight of a light gyroplane—a rotorcraft using an unpowered rotor in autorotation to develop lift and an engine-powered propeller to provide thrust. An original methodology of computational simulation of rotorcraft flight was developed and implemented. In this approach the aircraft motion equations are solved step-by-step, simultaneously with the solution of the Unsteady Reynolds-Averaged Navier–Stokes equations, which is conducted to assess aerodynamic forces acting on the aircraft. As a numerical optimization method, the BFGS (Broyden–Fletcher–Goldfarb–Shanno) algorithm was adapted. The developed methodology was applied to optimize the flight control procedures in selected stages of gyroplane flight in direct proximity to the ground, where proper control of the aircraft is critical to ensure flight safety and performance. The results of conducted computational optimizations proved the qualitative correctness of the developed methodology. The research results can be helpful in the design of easy-to-control gyroplanes and also in the training of pilots for this type of rotorcraft.
      Citation: Computation
      PubDate: 2018-02-06
      DOI: 10.3390/computation6010016
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 17: A Localized Meshless Technique for
           Generating 3-D Wind Fields

    • Authors: Darrell Pepper, Maria Ramos Gonzalez
      First page: 17
      Abstract: A localized meshless method is used to simulate 3-D atmospheric wind fields for wind energy assessment and emergency response. The meshless (or mesh-free) method with radial basis functions (RBFs) alleviates the need to create a mesh required by finite difference, finite volume, and finite element methods. The method produces a fast solution that converges with high accuracy, establishing 3-D wind estimates over complex terrain. The method does not require discretization of the domain or boundary and removes the need for domain integration. The meshless method converges exponentially for smooth boundary shapes and boundary data, and is insensitive to dimensional constraints. Coding of the method is very easy and can be done using MATLAB or MAPLE. By employing a localized RBF procedure, 3-D wind fields can be established from sparse meteorological data. The meshless method can be easily run on PCs and hand-held mobile devices. This article summarizes previous work where the meshless method has successfully simulated 3D wind fields over various environments, along with the equations used to obtain the simulations.
      Citation: Computation
      PubDate: 2018-02-08
      DOI: 10.3390/computation6010017
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 18: Coefficients Calculation in Pascal
           Approximation for Passive Filter Design

    • Authors: George Kasapoglu, Evangelia Karagianni, Michael Fafalios, Ioannis Koukos
      First page: 18
      Abstract: The recently modified Pascal function is further exploited in this paper in the design of passive analog filters. The Pascal approximation has non-equiripple magnitude, in contrast of the most well-known approximations, such as the Chebyshev approximation. A novelty of this work is the introduction of a precise method that calculates the coefficients of the Pascal function. Two examples are presented for the passive design to illustrate the advantages and the disadvantages of the Pascal approximation. Moreover, the values of the passive elements can be taken from tables, which are created to define the normalized values of these elements for the Pascal approximation, as Zverev had done for the Chebyshev, Elliptic, and other approximations. Although Pascal approximation can be implemented to both passive and active filter designs, a passive filter design is addressed in this paper, and the benefits and shortcomings of Pascal approximation are presented and discussed.
      Citation: Computation
      PubDate: 2018-02-14
      DOI: 10.3390/computation6010018
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 19: Effect of Carbon Concentration on the
           Sputtering of Carbon-Rich SiC Bombarded by Helium Ions

    • Authors: Xinghao Liang, Yang Li, Qiang Zhao, Zheng Zhang, Xiaoping Ouyang
      First page: 19
      Abstract: Silicon carbide (SiC) is considered as an important material for nuclear engineering due to its excellent properties. Changing the carbon content in SiC can regulate and control its elastic and thermodynamic properties, but a simulation study of the effect of carbon content on the sputtering (caused by the helium ions) of SiC is still lacking. In this work, we used the Monte-Carlo and molecular dynamics simulation methods to study the effects of carbon concentration, incidence energy, incident angle, and target temperature on the sputtering yield of SiC. The results show that the incident ions’ energy and angle have a significant effect on sputtering yield of SiC when the carbon concentration in SiC is around 62 at %, while the target temperature has a little effect on the sputtering yield of SiC. Our work might provide theoretical support for the experimental research and engineering application of carbon fiber-reinforced SiC that be used as the plasma-facing material in tokamak fusion reactors.
      Citation: Computation
      PubDate: 2018-02-14
      DOI: 10.3390/computation6010019
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 20: Implications of PCCA+ in Molecular

    • Authors: Marcus Weber
      First page: 20
      Abstract: Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ‘bound’ vs. ‘unbound’), although the process itself takes place in a continuous space. In this context, the formula χ = X A connects the micro-dynamics of the molecular system to its macro-dynamics. χ can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences.
      Citation: Computation
      PubDate: 2018-02-19
      DOI: 10.3390/computation6010020
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 21: The Role of Conformational Entropy in the
           Determination of Structural-Kinetic Relationships for Helix-Coil

    • Authors: Joseph Rudzinski, Tristan Bereau
      First page: 21
      Abstract: Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.
      Citation: Computation
      PubDate: 2018-02-26
      DOI: 10.3390/computation6010021
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 22: Optimal Data-Driven Estimation of
           Generalized Markov State Models for Non-Equilibrium Dynamics

    • Authors: Péter Koltai, Hao Wu, Frank Noé, Christof Schütte
      First page: 22
      Abstract: There are multiple ways in which a stochastic system can be out of statistical equilibrium. It might be subject to time-varying forcing; or be in a transient phase on its way towards equilibrium; it might even be in equilibrium without us noticing it, due to insufficient observations; and it even might be a system failing to admit an equilibrium distribution at all. We review some of the approaches that model the effective statistical behavior of equilibrium and non-equilibrium dynamical systems, and show that both cases can be considered under the unified framework of optimal low-rank approximation of so-called transfer operators. Particular attention is given to the connection between these methods, Markov state models, and the concept of metastability, further to the estimation of such reduced order models from finite simulation data. All these topics bear an important role in, e.g., molecular dynamics, where Markov state models are often and successfully utilized, and which is the main motivating application in this paper. We illustrate our considerations by numerical examples.
      Citation: Computation
      PubDate: 2018-02-26
      DOI: 10.3390/computation6010022
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 23: Ionic Liquids Treated within the Grand
           Canonical Adaptive Resolution Molecular Dynamics Technique

    • Authors: B. Shadrack Jabes, Christian Krekeler
      First page: 23
      Abstract: We use the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to examine the essential degrees of freedom necessary for reproducing the structural properties of the imidazolium class of ionic liquids. In this technique, the atomistic details are treated as an open sub-region of the system while the surrounding environment is modelled as a generic coarse-grained model. We systematically characterize the spatial quantities such as intramolecular, intermolecular radial distribution functions, other structural and orientational properties of ILs. The spatial quantities computed in an open sub-region of the system are in excellent agreement with the equivalent quantities calculated in a full atomistic simulation, suggesting that the atomistic degrees of freedom outside the sub-region are negligible. The size of the sub-region considered in this study is 2 nm, which is essentially the size of a few ions. Insight from the study suggests that a higher degree of spatial locality seems to play a crucial role in characterizing the properties of imidazolium based ionic liquids.
      Citation: Computation
      PubDate: 2018-02-28
      DOI: 10.3390/computation6010023
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 24: A Review of Numerical Modelling of
           Multi-Scale Wind Turbines and Their Environment

    • Authors: Katrina Calautit, Angelo Aquino, John Calautit, Payam Nejat, Fatemeh Jomehzadeh, Ben Hughes
      First page: 24
      Abstract: Global demand for energy continues to increase rapidly, due to economic and population growth, especially for increasing market economies. These lead to challenges and worries about energy security that can increase as more users need more energy resources. Also, higher consumption of fossil fuels leads to more greenhouse gas emissions, which contribute to global warming. Moreover, there are still more people without access to electricity. Several studies have reported that one of the rapidly developing source of power is wind energy and with declining costs due to technology and manufacturing advancements and concerns over energy security and environmental issues, the trend is predicted to continue. As a result, tools and methods to simulate and optimize wind energy technologies must also continue to advance. This paper reviews the most recently published works in Computational Fluid Dynamic (CFD) simulations of micro to small wind turbines, building integrated with wind turbines, and wind turbines installed in wind farms. In addition, the existing limitations and complications included with the wind energy system modelling were examined and issues that needs further work are highlighted. This study investigated the current development of CFD modelling of wind energy systems. Studies on aerodynamic interaction among the atmospheric boundary layer or wind farm terrain and the turbine rotor and their wakes were investigated. Furthermore, CFD combined with other tools such as blade element momentum were examined.
      Citation: Computation
      PubDate: 2018-03-05
      DOI: 10.3390/computation6010024
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 25: Dissipation Effects in Schrödinger and
           Quantal Density Functional Theories of Electrons in an Electromagnetic

    • Authors: Xiao-Yin Pan, Viraht Sahni
      First page: 25
      Abstract: Dissipative effects arise in an electronic system when it interacts with a time-dependent environment. Here, the Schrödinger theory of electrons in an electromagnetic field including dissipative effects is described from a new perspective. Dissipation is accounted for via the effective Hamiltonian approach in which the electron mass is time-dependent. The perspective is that of the individual electron: the corresponding equation of motion for the electron or time-dependent differential virial theorem—the ‘Quantal Newtonian’ second law—is derived. According to the law, each electron experiences an external field comprised of a binding electric field, the Lorentz field, and the electromagnetic field. In addition, there is an internal field whose components are representative of electron correlations due to the Pauli exclusion principle and Coulomb repulsion, kinetic effects, and density. There is also an internal contribution due to the magnetic field. The response of the electron is governed by the current density field in which a damping coefficient appears. The law leads to further insights into Schrödinger theory, and in particular the intrinsic self-consistent nature of the Schrödinger equation. It is proved that in the presence of dissipative effects, the basic variables (gauge-invariant properties, knowledge of which determines the Hamiltonian) are the density and physical current density. Finally, a local effective potential theory of dissipative systems—quantal density functional theory (QDFT)—is developed. This constitutes the mapping from the interacting dissipative electronic system to one of noninteracting fermions possessing the same dissipation and basic variables. Attributes of QDFT are the separation of the electron correlations due to the Pauli exclusion principle and Coulomb repulsion, and the determination of the correlation contributions to the kinetic energy. Hence, Schrödinger theory in conjunction with QDFT leads to additional insights into the dissipative system.
      Citation: Computation
      PubDate: 2018-03-06
      DOI: 10.3390/computation6010025
      Issue No: Vol. 6, No. 1 (2018)
  • Computation, Vol. 6, Pages 26: Recent Progress in First-Principles Methods
           for Computing the Electronic Structure of Correlated Materials

    • Authors: Fredrik Nilsson, Ferdi Aryasetiawan
      First page: 26
      Abstract: Substantial progress has been achieved in the last couple of decades in computing the electronic structure of correlated materials from first principles. This progress has been driven by parallel development in theory and numerical algorithms. Theoretical development in combining ab initio approaches and many-body methods is particularly promising. A crucial role is also played by a systematic method for deriving a low-energy model, which bridges the gap between real and model systems. In this article, an overview is given tracing the development from the LDA+U to the latest progress in combining the G W method and (extended) dynamical mean-field theory ( G W +EDMFT). The emphasis is on conceptual and theoretical aspects rather than technical ones.
      Citation: Computation
      PubDate: 2018-03-19
      DOI: 10.3390/computation6010026
      Issue No: Vol. 6, No. 1 (2018)
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