ALBERT

Description: In this paper, we present an algorithm for partitioning any given 2D domain into regions suitable for quadrilateral meshing. It is able to preserve the symmetry of the domain if any, and can deal with inner boundaries and multidomain geometries. Moreover, this method keeps the number of singularities at the junctions of the regions to a minimum. Although each part of the domain, being four-sided, can be easily meshed using a structured method, we provide a meshing process that guarantees near perfect quality for most quadrilaterals of the resulting mesh. The partitioning stage is achieved by solving a PDE-constrained equation based on the geometric properties of the domain boundaries. An analysis of the generated mesh quality is provided at the end, showcasing that the meshes obtained through our algorithm are especially suitable for finite element methods.

Description: This paper introduces a methodology for creating geometrically consistent subsurface simulation models, and subsequently tetrahedral finite element (FE) meshes, from geometric entities generated in gOcad software. Subsurface simulation models have an intrinsic heterogeneous characteristic due to the different geomechanics properties of each geological layer. This type of modeling should represent geometry of natural objects, such as geological horizons and faults, which have faceted representations. In addition, in subsurface simulation modeling, lower-dimension degenerated parts, such as dangling surfaces, should be represented. These requirements pose complex modeling problems, which, in general, are not treated by a generic geometric modeler. Therefore, this paper describes four important modeling capabilities that are implemented in a subsurface simulation modeler: surface re-triangulation, surface intersection, automatic volume recognition, and tetrahedral mesh generation. Surface re-triangulation is used for regenerating the underlying geometric support of surfaces imported from gOcad and of surface patches resulting from intersection. The same re-triangulation algorithm is used for generating FE surface meshes. The proposed modeling methodology combines, with some adaptation, meshing algorithms previously published by the authors. Two novel techniques are presented, the first for surface intersection and the second for automatic volume recognition. The main contribution of the present work is the integration of such techniques through a methodology for the solution of mesh generation problems in subsurface simulation modeling. An example illustrates the capabilities of the proposed methodology. Shape quality of generated triangular surface and tetrahedral meshes, as well as the efficiency of the 3D mesh generator, is demonstrated by means of this example.

Description: An automated approach to quadrilateral mesh generation with complex internal geometric feature constraints is presented in this paper. It can deal with all kinds of feature constraints such as internal holes, constraint lines, constraint points, density lines and density points, etc., and satisfy special requirements of mesh generation for numerical analysis. The quadrilateral mesh is generated based on the looping algorithm. As the core of the algorithm, the new splitting criteria are put forward to improve the quality and efficiency of mesh generation. The method of dealing with feature constraints is proposed by considering constraint lines and points, density lines and density points as internal holes with zero area. The method for generating boundary elements is also introduced to improve the element quality around the boundary and feature constraints. For the situation in which feature constraints subdivide the domain into sub-domains, an automatic determination method of sub-domain boundaries is presented. An improved looping algorithm is presented for 3D surface meshing with feature constraints. The determination of proper splitting plane and the handling of feature constraints are put forward. The program of quadrilateral mesh generation has been developed based on the method presented in this paper and successfully applied to mesh generation in several engineering fields.

Description: This paper aims to introduce a unified code for fluid flow modeling in complex channels reconstructed from imagery. Given a binary image of a cross-section or projection of planar connected channels with circular cross-sections, we wish to: (1) reconstruct a three-dimensional model of the boundary of the geometry, (2) establish boundary condition of the flow field, and (3) compute a fluid simulation based on a Cartesian grid. Our solution has the following advantages. First, we use the same mathematical tools throughout the process i.e. a level set function and a skeleton to describe the geometry. The skeleton of the geometry is essential in the imagery part to transform the 2D geometry into a 3D geometry but is also essential in the fluid flow part to construct a velocity field of reference for boundary conditions in the mechanical fluid flow model. Then, the integration of the geometry into the fluid mechanic code is simplified thanks to a Cartesian grid taking into account the geometry through the level set function. Finally, this work leads to a stand-alone code capable of simulating 3D flows in geometry reconstructed 2D images. We show its usefulness in applications to medical imagery (namely angiography) and bifluid flows in microchannels.

Description: This paper presents simulation methodology that combines a local nonmatching grid with a discrete fracture model. Designed for 2D and 3D multiphase flow simulations in standard simulators, the method handles matrix–matrix, fracture–fracture, and matrix–fracture connections in the context of an unstructured, local nonmatching grid. The grid is generated at the fracture intersections, enabling accurate modeling of small control volumes between connecting fractures. Grids are obtained simply by redistributing the volume of small control volumes surrounding the small control volumes, making the method computationally efficient. A unified method to calculate the interblock transmissibility is used for both matching and nonmatching mesh. An unstructured finite-volume graph-based reservoir simulator with a two-point flux approximation reads the new grid by making a simple modification to the graph of connections between the control volumes. The method requires no special treatment of fracture–fracture or matrix–fracture transmissibility calculations and has the flexibility to simulate any flow problem efficiently. Several 2D and 3D numerical examples demonstrate the method’s performance and accuracy. Both simple and complex fracture configurations are presented with various levels of geologic and fluid complexity. The numerical results are in good agreement with those of a reference solution obtained on a finely structured grid.

Description: Remeshing is an important problem in variety of applications, such as finite element methods and geometry processing. Surface remeshing poses some unique challenges, as it must deliver not only good mesh quality but also good geometric accuracy. For applications such as finite elements with high-order elements (quadratic or cubic elements), the geometry must be preserved to high-order (third-order or higher) accuracy, since low-order accuracy may undermine the convergence of numerical computations. The problem is particularly challenging if the CAD model is not available for the underlying geometry, and is even more so if the surface meshes contain some inverted elements. We describe remeshing strategies that can simultaneously produce high-quality triangular meshes, untangling mildly folded triangles and preserve the geometry to high-order of accuracy. Our approach extends our earlier works on high-order surface reconstruction and mesh optimization by enhancing its robustness with a geometric limiter for under-resolved geometries. We also integrate high-order surface reconstruction with surface mesh adaptation techniques, which alter the number of triangles and nodes. We demonstrate the utilization of our method to meshes for high-order finite elements, biomedical image-based surface meshes, and complex interface meshes in fluid simulations.

Description: This paper presents an anisotropic adaptive strategy for CFD that combines a nearly body-fitted mesh strategy with an iterative anisotropic adaptation to the flow solution. The nearly body-fitted mesh method consists in modelling embedded interfaces by a level-set representation in combination with local anisotropic mesh refinement and mesh adaptation (Quan et al. in Comput Methods Appl Mech Eng 268:65–81, 2014 ). The generated nearly body-fitted meshes are used to perform CFD simulations. Besides, anisotropic mesh adaptation based on the Hessian of the flow solution is used to improve the accuracy of the solution. We show that the method is beneficial in challenging CFD simulations involving complex geometries and time dependent flow, as it suppresses the need for the tedious process of body-fitted mesh generation, without altering the finite element formulation nor the prescription of boundary conditions. The methodology yields accurate flow solutions for a reasonable computational cost, despite very limited user interaction.

Description: In this paper, two PDE-based mapping operators for the generation of unstructured meshes are compared. While the Winslow operator allows the construction of valid meshes for most configurations, the functional-based operators based on area, length, orthogonality and their combinations provide a finer control on the resulting meshes. Two distinct discretization methods of the operators are also compared. An original approach using a finite difference scheme on unstructured meshes is implemented and compared to a finite volume formulation. While more complex to implement and control, mainly because of the cross-derivative terms which must be carefully discretized, the finite volume method yields a more robust and stable formulation that allows dealing with sharp curvature variations of the boundaries. Finally, a criterion for the mesh smoothness which has a global definition is presented in order to compare the smoothness of the resulting mesh obtained by different operators.

Description: Development and application of metal matrix composite materials and increased application of calculations, simulations and modeling in the area of semi-solid solidification ask for the knowledge of compocasting for these materials. In this study, a self-organizing hierarchical particle swarm optimizer is implemented for computational modeling and optimization of the compocast high strength and highly uniform Al matrix composites. The matrix of the composite was a 6061 Al alloy and the reinforcement was alumina particle (Al 2 O 3 p). Experimental results were obtained for hardness, tensile and fatigue properties of the Al alloys with different vol.% of micro-particles. The tensile strength of the composites increased considerably by increasing the reduction ratio in the cold rolling process. It is observed that the presence of reinforcement in the Al alloy degrades the low-cycle fatigue property when the Al matrix composites are subject to strain-controlled cyclic loading. The method combines position update rules, the standard velocity and the strengths of particle swarm optimization with the ideas of selection, crossover and mutation from GA.

Description: In this paper, we present formulae for evaluating differential quantities at vertices of triangular meshes that may approximate potential piecewise smooth surfaces with discontinuous normals or discontinuous curvatures at the joint lines. We also define the C 1 and C 2 discontinuity measures for surface meshes using changing rates of one-sided curvatures or changing rates of curvatures across mesh edges. The curvatures are computed discretely as of local interpolating surfaces that lie within a tolerance to the mesh. Together with proper estimation of local shape parameters, the obtained discontinuity measures own properties like sensitivity to salient joint lines and being scale invariant. A simple algorithm is finally developed for detection of C 1 or C 2 discontinuity joint lines on triangular meshes with even highly non-uniform triangulations. Several examples are provided to demonstrate the effectiveness of the proposed method.

Description: We propose simple and efficient optimization-based untangling strategies for 2D polygonal and 3D polyhedral meshes. The first approach uses a size-based mesh metric, which eliminates inverted elements by averaging element size over the entire mesh. The second method uses a hybrid quality metric, which untangles inverted elements by simultaneously averaging element size and improving element shape. The last method using a variant of the hybrid quality metric gives a high penalty for inverted elements and employs an adaptive sigmoid function for handling various mesh sizes. Numerical experiments are presented to show the effectiveness of the proposed untangling strategies for various 2D polygonal and 3D polyhedral meshes.

Description: In this paper, we present a Delaunay refinement algorithm for 4-dimensional ( \(\hbox {3D}+t\) ) segmented images. The output mesh is proved to consist of sliver-free simplices. Assuming that the hyper-surface is a closed smooth manifold, we also guarantee faithful geometric and topological approximation. We implement and demonstrate the effectiveness of our method on publicly available segmented cardiac images. Finally, we devise a tightly coupled parallelization technique to boost the performance of our 4-dimensional mesher, thereby taking advantage of the multi-core and many-core platforms already available in the market.

Description: Shape idealization transformations are very common operations when adapting a CAD component to FEA requirements. Here, an idealization approach is proposed that is based on generative shape processes used to decompose an initial B-Rep solid, i.e., extrusion processes with material addition are used to segment a solid. The corresponding extrusion primitives form the basis of candidate sub-domains for idealization and their connections conveyed through the generative processes they belong to, bringing robustness to set up the appropriate connections between idealized sub-domains. This is made possible because the connections between extrusion primitives have an explicit geometric representation and can be used to bound the connections between idealized sub-domains. Taking advantage of an existing construction tree as available in a CAD software does not help much because it may be complicated to use it for idealization processes because this tree structure is not unique. Using generative processes attached to an object that is no longer reduced to a single construction tree but to a graph containing all non-trivial construction trees, is more useful for the engineer to evaluate variants of idealization. From this automated decomposition, each primitive is subjected to a morphological analysis to define whether it can idealized or not. Subsequently, geometric interfaces between primitives form also a graph that can be used to process the connections between the idealized sub-domains generated from the primitives. These interfaces are taken into account to determine more precisely the idealizable sub-domains and their contours when primitives are incrementally merged to come back to produce the global morphological analysis of the initial object. A user-defined threshold is used to tune the morphological analysis with respect to further user parameters. Finally, the idealizable sub-domains and their connections are processed to locate the mid-surfaces and connect them using generic criteria that the user can tune locally using complementary criteria.

Description: Automotive companies continuously strive to design better products faster and more cheaply using simulation models to evaluate every possible aspect of the product. Multidisciplinary design optimization (MDO) can be used to find the best possible design taking into account several disciplines simultaneously, but it is not yet fully integrated within automotive product development. The challenge is to find methods that fit company organizations and that can be effectively integrated into the product development process. Based on the characteristics of typical automotive structural MDO problems, a metamodel-based MDO process intended for large-scale applications with computationally expensive simulation models is presented and demonstrated in an example. The process is flexible and can easily fit into existing organizations and product development processes where different groups work in parallel. The method is proven to be efficient for the discussed example and improved designs can also be obtained for more complex industrial cases with comparable characteristics.

Description: A new indirect quadrangular mesh generation algorithm which relies on sequential decision-making techniques to search for optimal triangle recombinations is presented. In contrast to the state-of-art Blossom-quad algorithm, this new algorithm is a good candidate for addressing the 3D problem of recombining tetrahedra into hexahedra.

Description: Haptic feedback usually involves two types of stimulation forces: forces that address the touch sense and forces that address the kinesthetic perception. Touch forces have a low intensity and a complex structure since they reflect contact phenomena where friction plays an important role. Therefore, they are quite difficult to simulate. Virtual prototyping with haptic feedback should ideally involve both types of forces, but the integration of the touch feeling makes the simulator very complex. In this paper, we present a novel concept for virtual prototyping in which the touch interaction is separated from the kinesthetic force feedback. This is possible using a prototype that has a real part undertaking the touch interaction and a virtual part that simulate feedback for the kinesthetic forces. In this way, a full haptic interaction with the virtual prototype is established by means of a device that provides a realistic simulation of the product. In order to illustrate the concept, several experiments have been carried out for the case of specific subsystems of a car, which are particularly involved in the driver–car interaction: steering system, clutch pedal and the gearshift. A user test is described in the last part as well as the conclusions of the research.

Description: A new closed advancing-layer method for generating high-aspect-ratio elements in the boundary-layer (BL) region is presented. This approach utilizes a recent connectivity optimization-based moving mesh strategy for deforming the volume mesh as the BL is inflated. It handles very efficiently BL front collision and produces a natural smooth anisotropic blending between colliding layers. Moreover, it provides a robust strategy to couple unstructured anisotropic mesh adaptation and high-aspect-ratio elements pseudo-structured BL meshes. The proposed method is directly compared to a well-established open advancing-layer method. Results for typical aerospace configurations are presented that provide a clear comparison between both methods as well as the effectiveness of the connectivity optimization-based moving mesh strategy. They show that the closed method yields similar results in terms of mesh quality and efficiency, and that the considered moving mesh strategy is an efficient and effective method for deforming the unstructured volume mesh.

Description: An alternative numerical method is developed to find stable and unstable periodic orbits of nonlinear dynamical systems. The method exploits the high efficiency of the Levenberg–Marquardt algorithm for medium-sized problems and has the additional advantage of being relatively simple to implement. It is also applicable to both autonomous and non-autonomous systems. As an example of its use, it is employed to find periodic orbits in the Rössler system, a coupled Rössler system, as well as an eight-dimensional model of a flexible rotor-bearing; problems which have been treated previously via two related methods. The results agree with the previous methods and are seen to be more accurate in some cases. A simple implementation of the method, written in the Python programming language, is provided as an Appendix.

Description: The structural health evaluation is performed by comparing the responses between the undamaged and damaged states. Because it is impractical to collect the response data at the intact state, it is important to establish the baseline data to be compared at measurement. The measured frequency response functions (FRFs) in the neighborhood of the first resonance frequency are transformed to the proper orthogonal mode (POM) corresponding to the first proper orthogonal value (POV). The POM data set at the first measurement on the damage-expected structure is taken as the baseline datum, and it is compared with another set extracted from the structure to attach a small mass on an element. The POM difference between two states is utilized as an index to detect damage. The FRF variation before and after a small mass attachment for the purpose of detecting the damage is investigated. The validity of the proposed method based on POM variation is illustrated in the damage detection of a two-dimensional frame structure model. It is shown that the damage region in the frame structure can be inferred by gradually narrowing from the global structure to the damage-expected element.

Description: The aim of this paper is to achieve the 3D reconstruction of blood vessels from a limited number of 2D transversal cuts obtained from scanners. This is motivated by the fact that data can be missing. The difficulty of this work is in connecting the blood vessels between some widely spaced cuts to produce the graph corresponding to the network of vessels. We identify the vessels on each transversal cut as a mass to be transported along a graph which allows to determine the bifurcation points of vessels. Specifically, we are interested in branching transportation Brasco et al. (SIAM J Math Anal 43(2):1023–1040, 2011 ) to model an optimized graph associated with the network of vessels. At this stage, we are able to reconstruct a 3D level set function by using the 2D level set functions given by the transversal cuts and the graph information. When the whole scanner data are available, a global reconstruction is proposed in a simple manner, without using the mass transfer problem.

Description: A novel second-order time integration algorithm for solving dynamic problems is presented. To demonstrate the abilities of this formulation, several linear and geometrical nonlinear structures are solved. The outcomes of authors’ technique are compared with the ones obtained by other researchers. The findings not only confirm the improved accuracy of the new scheme but also indicate that the suggested method remains stable when the trapezoidal rule fails to produce a stable solution. Effectively maximizing high-frequency numerical dissipation, without inducing excessive algorithmic damping in the important low-frequency region, is one of the proposed tactic merits. Spurious oscillations are removed, and small numerical dispersion error is achieved, when using this approach.

Description: This paper proposes a new iso-parametric tool path generation scheme for trimmed parametric surface based on two discrete parameterization techniques, namely, the Partial Differential Equation method and the newly developed “Boundary Interpolation method”. The efficiency of the scheme is measured in terms of path length and computational time for machining some typical surfaces. The side-steps and forward-steps have been formulated to suit the discrete nature of the surface representation. Conventionally the forward-step is calculated by approximating the cutting curve with osculating circle. Due to this approximation there is a possibility that the tolerance can go beyond given limit. In this paper an improved tolerance constraint method has been presented to keep the tolerance in forward-step under given value by considering the true profile of the cutting curve. Case studies show that the method presented here significantly improves the path profile by maintaining the tolerance limit.

Description: Econometric models for the forecast of tourism demand are developed in this paper. In order to assess the long-run trends concerning principal tourism generating countries, the Johansen's maximum likelihood techniques are applied. For a better assessment of the short-run trends, the estimated error correction terms are introduced to the first difference models to estimate the short-run relationships (Error Correction Models, ECMs). Based on the results given by the ECMs, fuzzy regression models are suggested and then compared in order to provide the forecasting ability of both techniques (Fuzzy and ECMs). Finally, for the evaluation of forecasting performance, the Theil's Inequality Coefficient is applied. Content Type Journal Article Pages 245-257 DOI 10.3233/JCM-140501 Authors G. Botzoris, Department of Civil Engineering, Democritus University of Thrace, Xanthi, Greece E. Varagouli, Department of Civil Engineering, Democritus University of Thrace, Xanthi, Greece V. Profillidis, Department of Civil Engineering, Democritus University of Thrace, Xanthi, Greece B. Papadopoulos, Department of Civil Engineering, Democritus University of Thrace, Xanthi, Greece P. Lathiras, Aristotle University of Thessaloniki, Thessaloniki, Greece Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: This paper examines the natural convection in a square enclosure filled with a water-Al_{2}O_{3} nanofluid which is under the influence of an external magnetic field. The bottom wall is uniformly heated and vertical walls are linearly heated whereas the top wall is well insulated. Lattice Boltzmann method (LBM) is applied to solve the coupled equations of flow and temperature fields. This study has been carried out for the pertinent parameters in the following ranges: Rayleigh number of the base fluid, Ra=10^{3} to 10^{5}, Hartmann number varied from Ha=0 to 60, the inclination angle of the magnetic field relative to the horizontal plane γ= 0° to 180° and the solid volume fraction of the nanoparticles between ϕ=0 and 6%. The results show that the heat transfer rate increases with an increase of the Rayleigh number but it decreases with an increase of the Hartmann number. Also for Ra ⩾ 5 × 10^{4} and for the range of Hartmann number study, we note that the heat transfer and fluid flow depends strongly upon the direction of magnetic field. In addition, according the Hartmann number, it observed that the magnetic field direction controls the effects of nanoparticles. Content Type Journal Article Pages 291-313 DOI 10.3233/JCM-140503 Authors Ahmed Mahmoudi, Unité de Recherche Matériaux, Energie et Energies Renouvelables, Faculté des Sciences de Gafsa, Gafsa, Tunisie Imen Mejri, Unité de Recherche Matériaux, Energie et Energies Renouvelables, Faculté des Sciences de Gafsa, Gafsa, Tunisie Mohamed AmmarAbbassi, Unité de Recherche Matériaux, Energie et Energies Renouvelables, Faculté des Sciences de Gafsa, Gafsa, Tunisie Ahmed Omri, Unité de Recherche Matériaux, Energie et Energies Renouvelables, Faculté des Sciences de Gafsa, Gafsa, Tunisie Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: Based on Petković-Ilić-Džunić method [3], we derive a family of three-step eighth-order Steffensen type iterative methods for solving nonlinear equations. The new methods without memory use two suitable parametric functions at the second and third steps and are free from any derivatives. Per iteration the new methods require four functional evaluations, which implies that the efficiency index of the new methods is 1.682. The advantage of the new methods is that the computing speed of the new methods is faster than that of other eighth-order Steffensen type methods without memory. Numerical examples are made to show the performance of our methods and support the developed theory. Content Type Journal Article Pages 277-287 DOI 10.3233/JCM-140505 Authors Xiaofeng Wang, School of Mathematics and Physics, Bohai University, Jinzhou, Liaoning, China Tie Zhang, College of Sciences, Northeastern University, Shenyang, Liaoning, China Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: Disaggregate mode choice models estimation, which are used for evaluating the ridership share on intercity travel service and for identifying modes which will lead to an upgraded traveler's service, constitutes a critical part of evaluating alternative travel service proposals to intercity travel. The aim of this paper is to estimate the choice of mode in intercity travel demand. Disaggregate logit models are estimated by using data collected in order to investigate the passengers' behavior of the broader region under study. The final models are applicable on regional level and have statistics within acceptable region. Content Type Journal Article Pages 259-268 DOI 10.3233/JCM-140502 Authors E.G. Varagouli, Department of Civil Engineering, Democritus University of Thrace, Komotini, Greece. E-mail: evarggo@civil.duth.gr Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: In this paper, the solution of fractional Riccati differential equation by using the operational matrix of shifted Legendre polynomial is discussed. The properties of shifted Legendre polynomials together with the Caputo fractional derivative are used to reduce the problem to the solution of nonlinear algebraic equations. Also the theoretical analysis of shifted Legendre polynomial method such as convergence and error analysis has been discussed. The illustrative examples demonstrate its applicability, validity and simplicity of the approximation scheme. Content Type Journal Article Pages 229-243 DOI 10.3233/JCM-140489 Authors K. Krishnaveni, Department of Mathematics, School of Humanities and Sciences, Sastra University, Thanjavur, Tamilnadu, India K. Kannan, Department of Mathematics, School of Humanities and Sciences, Sastra University, Thanjavur, Tamilnadu, India S. Raja Balachandar, Department of Mathematics, School of Humanities and Sciences, Sastra University, Thanjavur, Tamilnadu, India Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: The basic formalism of the MR-AQCC method is presented which is basically a size extensivity corrected MR-CI procedure. The correction is applied in form of a diagonal shift which allows easy implementation of the method into any MR-CI programs and makes the calculation on excited states also possible. Accuracy of the method is discussed. To show the applicability of the method we present the first results of our systematic study on the proton transfer in 7-azaindol. We conclude that inclusion of dynamic correlation is essential to get reliable energy differences and potential energy surfaces for this process. Content Type Journal Article Pages 457-467 DOI 10.3233/JCM-2002-23-422 Authors Péter G. Szalay, Department of Theoretical Chemistry, Eötvös Loránd University Imre Berente, Department of Theoretical Chemistry, Eötvös Loránd University Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Solvent, effect in both quantum and classical calculations are accurately described by the Polarizable Continuum Model (PCM) whose electrostatic equations can be solved on the molecular surface by finite elements approximation. The GePol algorithm for the definition of finite elements molecular surface has been revisited, improved and reimplemented from scratch. We achieved linear scaling computational cost thus extending the range of applicability of the PCM approach to very large molecular systems. Content Type Journal Article Pages 469-474 DOI 10.3233/JCM-2002-23-423 Authors G. Scalmani, Dipartimento di Chimica, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, via Cintia, I-80126 Napoli, Italy N. Rega, Dipartimento di Chimica, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, via Cintia, I-80126 Napoli, Italy M. Cossi, Dipartimento di Chimica, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, via Cintia, I-80126 Napoli, Italy V. Barone, Dipartimento di Chimica, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, via Cintia, I-80126 Napoli, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Isotopic separation factors of lithium ion complexed by crown-ethers are obtained from statistical mechanics. The effect of the organic arm which links the crown-ether to a silica matrix is considered. Ab initio HF/6-31+G * calculations, PM3 semiempirical calculations and hybrid quantum mechanics/molecular mechanics PM3/MM Molecular Dynamics simulations have been performed. In vacuum, it is found that 7 Li is better complexed than 6 Li by the crown-ether with or without its organic arm, in contrast to what is experimentally observed by liquid chromatography with ethanol solvent and crown-ethers grafted on silica. To model the solvent effect, some ethanol molecules are first included in the PM3 calculations to solvate the free lithium isotopes and the lithium isotopes complexed by the crown-ether. The method reproduces the observation that 6 Li isotope is more complexed than 7 Li, but the hierarchy of the experimental separation factor in the crown-ether series is not correctly recovered. The PM3/MM Molecular Dynamics simulations of the crown-ether 12C4 system show that when taking into account the effect of the organic arm, it is possible to find a separation factor in agreement with the experimental result. Content Type Journal Article Pages 451-456 DOI 10.3233/JCM-2002-23-421 Authors C. Millot, Equipe de chimie et biochimie théorique, UMR CNRS-UHP no 7565, Université Henri Poincaré – Nancy 1, Faculté des Sciences et Techniques, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-lès-Nancy Codex, France F. Dehez, Equipe de chimie et biochimie théorique, UMR CNRS-UHP no 7565, Université Henri Poincaré – Nancy 1, Faculté des Sciences et Techniques, Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-lès-Nancy Codex, France Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: This paper describes the design and implementation of abiGrid, a grid-based tool to enhance the scientific collaboration among different research groups of Quantum Chemists. The goal of abiGrid is to permit the use and interchange of home-made programs, while maintaining the individuality of the different codes that, as research tools, are subjected to changes and evolution. The research activity of the partners is focused on orbital localization in a Multi-Reference context, as a necessary step towards the development of efficient methods for the treatment of large quasi-degenerate systems. Central points of the project are the design of a Common Data format, and an extensive use of the Grid technology. Content Type Journal Article Pages 417-422 DOI 10.3233/JCM-2002-23-417 Authors Elda Rossi, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno (BO), Italy Andrew Emerson, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno (BO), Italy Stefano Evangelisti, Laboratoire de Physique Quantique, UMR 5626, Université Paul Sabatier, 118 Route de Narbonne, 41062 Toulouse CEDEX, France Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: The gas-phase interactions of H 3 C-CH 2 -CH 3 , H 2 C=C(H)XH 3 and HC≡C-XH 3 (X=C, Si, Ge) with Cu + have been investigated through the use of B3LYP/6-311+G(2df,2p) calculations. The most stable complexes are stabilized through agostic interactions between the metal cation and the hydrogen atoms of the XH 3 group. Only when the neutral presents a C≡C triple bond the conventional π-complexes are slightly more stable than those exhibiting agostic interactions. The nature of these non-conventional bonds is analyzed in terms of the topology of the charge density and second order orbital interactions. The strength of these bonds increases with the hydride character of the XH hydrogens explaining the fact that while propene and the Si- and Ge-containing analogs have similar Cu + binding energies, ethylsilane and ethylgermane are predicted to bind Cu + much more strongly than propane. Concomitantly, a significant weakening of the X-H linkages involved in the bond reflected in a very large red shifting of the X-H stretching frequency is systematically observed. Content Type Journal Article Pages 411-416 DOI 10.3233/JCM-2002-23-416 Authors Inés Corral, Departamento do Química, C-9. Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain Otilia Mó, Departamento do Química, C-9. Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain Manuel Yáñez, Departamento do Química, C-9. Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: The resonance Raman (RR) spectra of nickel bis-dimetliylglyoxime (NiDMG) were calculated in the framework of the transform theory of RR scattering by means of the Rush and Peticolas approximation in combination with density functional theory (DFT). The 1 1 Bu and 1 1 Au excited state geometries, required by this approach, were optimised within time-dependent DFT at the B3LYP and B3P86 levels of theory, using a Newton-Raphson algorithm where the first and second derivatives of the molecular excited state energies were calculated numerically through finite difference approximations. The B3LYP ground state force field was scaled with a set of global scaling factors that correct for errors arising from the quantum chemical method and the harmonic approximation. Comparison between the experimental RR spectra of NiDMG obtained with 413 nm excitation and those calculated in resonance with the transitions to the 1 1 Bu and 1 1 Au states show a good agreement for the most intense RR bands. Content Type Journal Article Pages 405-410 DOI 10.3233/JCM-2002-23-415 Authors Maria-Andrea Mroginski, Max-Planck-Institut für Strahlenchemie, Stiftstr. 34–36, D-45470 Mülheim an der Ruhr, Germany Franz Mark, Max-Planck-Institut für Strahlenchemie, Stiftstr. 34–36, D-45470 Mülheim an der Ruhr, Germany Peter Hildebrandt, Max-Planck-Institut für Strahlenchemie, Stiftstr. 34–36, D-45470 Mülheim an der Ruhr, Germany Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Hartree-Fock and MP2 calculations for the dipole moment μ and the dipole polarizabilities of uracil, using optimized geometries, and the 6-31+G(d,p) and 6-31+G(d * ,p) (d = 0.05) basis sets, have been performed. The experimental μ of uracil is reproduced with the MP2/6-31++G(3d,3p) methodology. The calculated values of dipole polarizability α are consistent with MP2 calculations of literature. Prediction for the β first- and γ second-hyperpolarizabilities of uracil are reported. Comparison to MP2 calculations between the employed basis sets, shows that 6-31+G(d * ,p) results leads to values of the β v and γ ave that are 20 % and 42 % larger than the obtained with the standard basis set. The proposed values for these properties of uracil are 45.1 au and 12787 au, respectively. Content Type Journal Article Pages 423-430 DOI 10.3233/JCM-2002-23-418 Authors Humberto Soscún, Laboratorio de Química Inorgánica Teórica, Departamento de Química, Facultad Experimental de Ciencias, La Universidad del Zulia, Ap. 526, Grano de Oro, Módulo No.2, Maracaibo, Venezuela Elba Manrique, Laboratorio de Química Inorgánica Teórica, Departamento de Química, Facultad Experimental de Ciencias, La Universidad del Zulia, Ap. 526, Grano de Oro, Módulo No.2, Maracaibo, Venezuela Javier Hernández, Laboratorio de Química Inorgánica Teórica, Departamento de Química, Facultad Experimental de Ciencias, La Universidad del Zulia, Ap. 526, Grano de Oro, Módulo No.2, Maracaibo, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Recent, work in the field of biological photoreceptors has demonstrated that computational chemistry can be successfully applied to ultrafast photobiological problems. Here we revise the results of the photoisomerization path mapping of the protonated Schiff base of retinal: the chromophore of rhodopsin proteins. These studies have produced the two-state/two-mode model which provides a rationale for the photon-induced molecular motion in the isolated retinal chromophore. Such model represents a substantial revision of the previous models for the primary event in vision in animals and light driven proton-pumping in halobacteriae. New computational results will be presented, which model the effects of an external counterfoil on the photoisomerization paths. Energetic, electronic, stereoselectivity control and tuning-effects will be analyzed and discussed in terms of counterfoil positions. Both solution and protein experimental data are revised using the new reactivity model. Content Type Journal Article Pages 431-439 DOI 10.3233/JCM-2002-23-419 Authors Marco Garavelli, Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy Fernando Bernardi, Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy Alessandro Cembran, Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy Massimo Olivucci, Istituto di Chimica Organica, Università di Siena, Via Aldo Moro, I-53100 Siena, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: In this paper we report the development of a new approach which can be used to improve supermolecule ab initio intermolecular potentials. It involves combining quantities obtained from low-level dimer calculations (exchange and coulomb energies) with quantities obtained from high-level monomer calculations (charge density overlaps, first-order Coulomb interaction energies and dispersion energy coefficients) in order to estimate the resulting potential energy surfaces at the high level of theory. The level of theory which can be used for both monomer and dimer calculations will increase in time. Therefore, the definitions of ‘low’ and ‘high’ level are flexible and depend on technological limitations: ‘low’ level must be computationally cheap enough to use in thousands of dimer calculations for multidimensional potential energy surfaces, and ‘high’ level is required only in a few monomer calculations. We present results for three homonuclear (He 2 , Ne 2 , Ar 2 ) and three heteronuclear (He-Ne, He-Ar, Ne-Ar) rare gas dimers using the MP2 method as the ‘low’ level of theory and the QCISD approach as the ‘high’ level. We compare the extrapolated results with the literature data available for ground state potential energy curves of these dimers. Content Type Journal Article Pages 391-397 DOI 10.3233/JCM-2002-23-413 Authors Elena Bichoutskaia, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK Matthew P. Hodges, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK Richard J. Wheatley, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: First-principles computer simulations of the metcar Ti 8 C 12 allow one to identify the geometrical structure of the clusters studied experimentally. Indeed, the combination of predictive computer simulations and experimental measurements of the vibrational spectra of clusters offers a viable tool for structural identification of atomic clusters. Content Type Journal Article Pages 399-403 DOI 10.3233/JCM-2002-23-414 Authors G.K. Gueorguiev, Departamento de Fíisica da Universidade, P-3004-516 Coimbra, Portugal J.M. Pacheco, Departamento de Fíisica da Universidade de Lisboa, Complexo Interdisciplinar, Av. Prof. Gama Pinto 2, P-1649-003 Lisboa Codex, Portugal Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Variational and Perturbative CAS-SCF-type algorithms based on molecular orbitals that, preserve their physical nature during the iterative process are discussed. The methods are based on the iterative diagonalization of the one-body reduced density matrix. If localized guess orbitals are used, the locality property is kept by the final orbitals. The formalism can be used to reduce the number of active orbitals in CAS-SCF calculations on large systems, and in general to have a better control on the physical nature of the active space. The reduction from a complete to selected reference space is also possible in the case of Configuration-Interaction calculations. Content Type Journal Article Pages 385-389 DOI 10.3233/JCM-2002-23-412 Authors Celestino Angeli, Dipartimento di Chimica, Universitá di Ferrara, via Borsari 46, I-44100 Ferrara, Italy Carmen J. Calzado, Departamento de Quimica Fisica, Universidad de Sevilla - c/ Profesor Garcia Gonzalez, s/n. E-41012 Sevilla, Spain Renzo Cimiraglia, Dipartimento di Chimica, Universitá di Ferrara, via Borsari 46, I-44100 Ferrara, Italy Stefano Evangelisti, Laboratoire de Physique Quantique, UMR 5626, Université Paul Sabatier, 118, Route de Narbonne, 31062 Toulouse CEDEX, France Nathalie Guihéry, Laboratoire de Physique Quantique, UMR 5626, Université Paul Sabatier, 118, Route de Narbonne, 31062 Toulouse CEDEX, France Jean-Paul Malrieu, Laboratoire de Physique Quantique, UMR 5626, Université Paul Sabatier, 118, Route de Narbonne, 31062 Toulouse CEDEX, France Daniel Maynau, Laboratoire de Physique Quantique, UMR 5626, Université Paul Sabatier, 118, Route de Narbonne, 31062 Toulouse CEDEX, France Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: The aggregation of molecules characterized by some degree of rigidity, in amorphous systems, leads to the presence of voids that are responsible for important properties of the amorphous material. One example is the diffusion of small atoms or molecules through polymers or other materials, which is of relevance in the fabrication of materials for packaging, or for efficient gas sensors and biosensors. A second example, is the physisorption of hydrogen molecules in carbonaceous materials, of relevance for the utilization of hydrogen as a pollution-free energy carrier. In this work we present a computational study, carried out with the help of molecular mechanics and molecular dynamics simulations, of the diffusion and storage of gas particles inside samples of amorphous aggregates: in particular we concentrate on the diffusion of He into the branched structure of polypyrrole, and simulate the hydrogen storage capacity of aggregates of three-dimensional polyphenylene dendrimers. Content Type Journal Article Pages 441-449 DOI 10.3233/JCM-2002-23-420 Authors Fabrizia Negri, Universita' di Bologna, Dipartimento di Chimica ‘G. Ciamician’, Via F. Selmi, 2 40126 Bologna, Italy Emanuela Emanuele, Universita' di Bologna, Dipartimento di Chimica ‘G. Ciamician’, Via F. Selmi, 2 40126 Bologna, Italy Aurora Calabretta, Universita' di Bologna, Dipartimento di Chimica ‘G. Ciamician’, Via F. Selmi, 2 40126 Bologna, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: In this paper we describe developed grid tools for qunatum chemical and biomolecular applications. We have used Unicore infrastructure as framework for development dedicated user interface to the Gaussian98, Amber 6.0, Car-Parrinello Molecular Dynamics Code as well as interface to Protein Data Bank. The user interface is integrated with the UNICORE client based on plugin mechanism which provides general grid functionality such as single login, job submission and control mechanism. Content Type Journal Article Pages 369-375 DOI 10.3233/JCM-2002-23-410 Authors Jaroslaw Pytliński, ICM Warsaw University, Pawińskiego 5a, 02-106 Warsaw, Poland Łukasz Skorwider, ICM Warsaw University, Pawińskiego 5a, 02-106 Warsaw, Poland Valentina Huber, Research Center Jülich, D-52425 Jülich, Germany Michał Wroński, Faculty of Mathematics and Computer Science, N. Copernicus University, Chopina 12/18, 87-100 Toruń, Poland Piotr Bała, Faculty of Mathematics and Computer Science, N. Copernicus University, Chopina 12/18, 87-100 Toruń, Poland Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Time-dependent, quantum mechanical values of the reactive probability for the Li + HF(v = 0, j = 0) → LiF + H system have been calculated for a sufficiently extended interval of energy. From these values estimates of the reactive cross section were obtained using an energy shifting model. A comparison of theoretical predictions with experimental data is also given. Content Type Journal Article Pages 361-367 DOI 10.3233/JCM-2002-23-409 Authors Valentina Piermarini, Dipartimento di Chimica, Università di Perugia, Perugia, Italy Stefano Crocchianti, Dipartimento di Chimica, Università di Perugia, Perugia, Italy Antonio Laganà, Dipartimento di Chimica, Università di Perugia, Perugia, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Natural Computing is a general term referring to computing going on in nature and computing inspired by nature. When complex phenomena going on in nature are viewed as computational processes, our understanding of these phenomena and of the essence of computation is enhanced. In this way one gains valuable insights into both natural sciences and computer science. Ciliates, a very ancient group of single cell organisms, have evolved extraordinary ways of organizing, manipulating and replicating their DNA. The way that ciliates transform genes from their micronuclear (storage) form into their macronuclear (expression) form, called gene assembly, is very interesting from the computational point of view. Current research in gene assembly is an example of flourishing interdisciplinary research involving computer scientists and molecular biologists. This paper discusses (in tutorial fashion) some central ideas of this research. Content Type Journal Article Pages 343-349 DOI 10.3233/JCM-2002-23-407 Authors G. Rozenberg, Leiden Institute of Advanced Computer Science, Leiden University, The Netherlands Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: We discuss a prototype of a Problem Solving Environment for an a priori Molecular Simulator for the study of Chemical reactivity implemented on a computational Grid. The Environment is implemented using Web technologies and makes use of Freesoftware packages. Content Type Journal Article Pages 377-383 DOI 10.3233/JCM-2002-23-411 Authors Osvaldo Gervasi, Department of Mathematics and Informatics, University of Perugia, via Vanvitelli, 1, I-06124 Perugia, Italy Antonio Laganà, Department of Chemistry, University of Perugia, via Elce di Sotto, 8, I-06123 Perugia, Italy Francesco Sportolari, CASI, University of Perugia, via G.Duranti 1/A, I-06125 Perugia, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Energy minimized even-tempered basis sets for 4-component relativistic quantum chemical calculations have been derived for Kr, Xe, and Rn. In order to reach the same accuracy as previously derived double zeta basis sets, a considerably larger number of functions is needed for the even-tempered sets. The even tempered sets are also unsuited for dual family type basis sets. Content Type Journal Article Pages 335-341 DOI 10.3233/JCM-2002-23-406 Authors Knut Fægri, Laboratoire do Physique Quantique, IRSAMC, Universite Paul Sabatier, 118 Route de Narbonne, F - 31062 Toulouse CEDEX, France Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: In this paper we have reported the results of theoretical investigations at the DFT level on the mechanism of some representative organometallic reactions. In all cases the non-local hybrid B3LYP functional has been used. The reactions examined here are: (a) the cyclopropanation reactions promoted by transition metal complexes and (b) the nickel-catalyzed carbonylation reactions. In the former case we have considered in details the Simmons-Smith reaction and the cyclopropanation promoted by palladium complexes. It has been found that the active cyclopropanating reagent is always a carbenoid species [L]-M-CH 2 -X (I., X = ligands) and that the cyclopropanation promoted by palladium complexes proceeds either via a concerted mechanism or a multi-step mechanism involving palladacyclobutane intermediates. For the carbonylation reactions we have examined in details the mechanism of the insertion of a CO molecule into a nickel-carbon bond. This step corresponds to a complicated process involving either four-coordinated or five-coordinated nickel complexes. Content Type Journal Article Pages 319-333 DOI 10.3233/JCM-2002-23-405 Authors Andrea Bottoni, Dipartimento di Chimica “G.Ciamician”, Universita' di Bologna, via Selmi 2, 40126 Bologna, Italy Fernando Bernardi, Dipartimento di Chimica “G.Ciamician”, Universita' di Bologna, via Selmi 2, 40126 Bologna, Italy Gian Pietro Miscione, Dipartimento di Chimica “G.Ciamician”, Universita' di Bologna, via Selmi 2, 40126 Bologna, Italy Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: The last couple of years it lias become more and more clear that lateral interactions (interactions between adsorbates) play an important role in the kinetics of surface reactions. We work on the determination of these interactions, and on methods to predict the kinetics including these interactions. Our main method is Dynamic Monte Carlo. With this method we can simulate all reactions on a surface with between 10 4 and 10 8 reactive sites for about 10 2 -10 3 seconds. The simulations yield predictions of the kinetics that are exact for a given model of the surface reactions. As input we need rate constants (prefactors and activation energies) and lateral interactions. These are either obtained by fitting to experimental results or by calculating them using Density-Functional Theory. We use Evolutionary Computation methods to vary and optimize the kinetic parameters when fitting to experiments. Content Type Journal Article Pages 351-359 DOI 10.3233/JCM-2002-23-408 Authors A.P.J. Jansen, Schuit Institute of Catalysis, ST/SKA, Eindhoven University of Technology P. O. Box 513, 5600 MB Eindhoven, The Netherlands W.K. Offermans, Schuit Institute of Catalysis, ST/SKA, Eindhoven University of Technology P. O. Box 513, 5600 MB Eindhoven, The Netherlands Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Ab initio Density Functional Theory calculations are presented on cyclization and hydrogen abstraction reactions of various polycyclic aromatic hydrocarbons (PAH) which are important for numerous applications. Attention is focussed on the influence of the local structure of the cluster on the reactivity of these elementary radical processes. This is done by calculating the kinetic parameters by means of Transition State Theory. For ring-closure reactions the activation energies are largely affected by the local structure of the polycyclic aromatic hydrocarbon. The variations can be explained in terms of the aromaticity of the reactants and steric hindrance between the attacking radical and the substrate. The aromaticity of the various PAHs can be efficiently probed by various magnetic properties (proton chemical shifts, magnetic susceptibilities and nuclear-independent chemical shifts (NICS)). A correlation is found between the variations in aromaticity during a chemical reaction and the reaction barrier. Reaction barriers for hydrogen abstraction reactions are quite insensitive for the local PAH structure. Variations in the preexponential factor must be attributed to the presence of low vibrational internal rotations or various bending modes in the clusters. Content Type Journal Article Pages 315-318 DOI 10.3233/JCM-2002-23-404 Authors V. Van Speybroeck, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium K. Hemelsoet, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium M. Waroquier, Laboratory of Theoretical Physics, Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium G.B. Marin, Laboratorium voor Petrochemische Techniek, Ghent University, Krijgslaan 286-S5, B-9000 Gent, Belgium Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 2 Journal Issue Volume 2, Number 3-4 / 2002

Description: Load balancing is an important aspect of Grid resource scheduling. This paper attempts to address the issue of load balancing in a Grid, while maintaining the resource utilization and response time for dynamic and decentralized Grid environment. Here, to its optimum value, a hierarchical load balancing technique has been analysed based on variable threshold value. The load is divided into different categories, such as lightly loaded, under-lightly loaded, overloaded, and normally loaded. A threshold value, which can be found out using load deviation, is responsible for transferring the task and flow of workload information. In order to improve response time and to increase throughput of the Grid, a random policy has been introduced to reduce the resource allocation capacity. The proposed model has been rigorously examined over the GridSim simulator using various parameters, such as response time, resource allocation efficiency, etc. Experimental results prove the superiority of the proposed technique over existing techniques, such as without load balancing, load balancing in enhanced GridSim.

Description: An inverse analysis methodology for determining the parameters of the kinematic law of sheet metals is proposed. The sensitivity of the load versus displacement curves, obtained by reverse shear tests of rectangular and notched specimens, to the kinematic law parameters are studied following a forward analysis, based on finite element simulations. Afterwards, an inverse analysis methodology using a gradient-based Levenberg–Marquardt method is established, by evaluating the relative difference between numerical and experimental results of the shear test, i.e. the load evolution in function of the displacements of the grips. The use of a notched specimen is proposed in order to allow an easy and suitable numerical representation of the boundary conditions of the shear experimental test. This methodology has proven to be appropriate for determining the parameters of the kinematic hardening law.

Description: In this paper, we have investigated the role of dependencies in the design process of mechatronic products. Since explicit modeling of dependencies is largely considered unnecessary today, current languages do not support dependency modeling due to lack of sufficiently expressive language constructs. However, this paper argues that modeling dependencies is important in managing the overall design process. The paper highlights dependencies between two important viewpoints: system design and mechanical design. We have looked closely at how mechanical design (supported by CAD tools) establishes a backbone for the overall design concept. Mechanical design cannot be isolated from other design activities, and the mismanagement of dependencies there leads to problems in other domains too. To illustrate the process, the paper presents an example of modeling dependencies between system hierarchy in OMG SysML™ and the CAD assembly in Solid Edge for a mechatronic design example. The paper presents two different approaches to capturing dependencies—using a general purpose modeling language such as SysML and using a domain specific modeling language (DSML). We argue for using a DSML instead of a general purpose language and provide a DSML called the dependency modeling language (DML). An example DML model for a two degree of freedom robot use case is discussed. The paper also illustrates the complete process of capturing dependencies in a general purpose modeling language like SysML, which served as a good exercise on how to fetch data from a CAD tool and how to represent dependencies inside a significantly different modeling language. Lessons learned from doing this were applied to the construction of DML. Our aim for the future is to reduce the human effort required to build dependency models. Machine learning techniques and automated model transformations are valuable techniques to support this cause.

Description: In this research, influences of two factors in adaptive metamodeling, noise level of samples and initial size of samples, are investigated through comparative study. Two cases of adaptive metamodeling considering the best output point for optimization and the best fit in a specific output parameter space are considered. Three different metamodels, kriging, radial basis function, and multivariate polynomial, are employed in this study. Various test functions are used to create the sample data and evaluate the quality and efficiency of the adaptive metamodeling methods considering influences of noise and initial size of samples. The results of this research provide guidelines for selecting appropriate adaptive metamodeling methods to solve various engineering problems. Effectiveness of the developed guidelines has been demonstrated through case study applications.

Description: In geometric modeling, surface parameterization plays an important role for converting triangle meshes to spline surfaces. Parameterization will introduce distortions. Conventional parameterization methods emphasize on angle-preservation, which may induce huge area distortions and cause large spline fitting errors and trigger numerical instabilities.To overcome this difficulty, this work proposes a novel area-preserving parameterization method, which is based on an optimal mass transport theory and convex geometry. Optimal mass transport mapping is measure-preserving and minimizes the transportation cost. According to Brenier’s theorem, for quadratic distance transportation costs, the optimal mass transport map is the gradient of a convex function. The graph of the convex function is a convex polyhedron with prescribed normal and areas. The existence and the uniqueness of such a polyhedron have been proved by the Minkowski-Alexandrov theorem in convex geometry. This work gives an explicit method to construct such a polyhedron based on the variational principle, and formulates the solution to the optimal transport map as the unique optimum of a convex energy. In practice, the energy optimization can be carried out using Newton’s method, and each iteration constructs a power Voronoi diagram dynamically. We tested the proposal algorithms on 3D surfaces scanned from real life. Experimental results demonstrate the efficiency and efficacy of the proposed variational approach for the optimal transport map.

Description: A binary system in solid solution when is quenched at a temperature under the solubility limit, shows a structural instability that disappears when said system reaches equilibrium. In the process of reaching stability, a number of microstructural modifications or fluctuations in concentration occur, which tend to generate a decrease in the free energy of the system. Critical fluctuations arise, prompting the association of critical size clusters, from which the growth of the phases responsible for final equilibrium is produced. Such proposal falls completely under the nucleation and growth theory where the first stage – before critical fluctuation appears, occurs at nucleation, whereas the latter stage corresponds to growth and coalescence of the clusters. The evaporation and condensation theory has been adapted so that the process of phase transformation is simulated while considering different evolution pathways from solid solution to the phase of equilibrium. Because the nucleation phase is energetically unstable, it is characterized by each cluster in that stage, while every cluster in the metastable or stable growth phase is grouped via the corresponding transformed fraction, which includes every metastable or stable cluster formed for a given aging time and temperature, thus allowing phase transformation to be expressed as one equation per phase plus the nucleation equations instead of an equation per cluster of different size. This paper expands on the calculation of the problem, determining the effect of the different parameters affecting phase kinetics in the Fe-C system for very low concentrations of C. Content Type Journal Article Pages 179-194 DOI 10.3233/JCM-140495 Authors M. Gómez, Grupo de Física de Metales, Dpto. de Física, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Cumaná, Venezuela N. Luiggi A., Grupo de Física de Metales, Dpto. de Física, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Cumaná, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: This paper presents specific procedures for locally refining nodal connectivity of two-dimensional unstructured triangular meshes to improve the quality of the mesh as well as to increase solution accuracy and computational speed. Details of the procedure are outlined along with a discussion of similar work, and an example problem from hydrodynamics is shown.

Description: The structure graphene has a semiconductor character, however this property can be modified by the incorporation of defects produced by desorption of carbon atoms or adsorption on the surface metals. Therefore has an importance in areas of catalysis, new generations of batteries and nanoelectronics. This work was done through a theoretical study of graphene with defects and its variation in the electrical conduction. The optimized circumcoronene formed the basis for the molecules with vacancies and doped with transition metals: Fe and Cu. Calculations were made using the B3PW91 hybrid functional theory of the density and the LANL2DZ basis set. In all forms is calculated NBO electrical charges, energy gap value, geometric parameters, electrostatic potential to the last occupied molecular orbital and determined the stability of the structures by adsorption energies for metals and the desorption for vacancy defects. All structures showed a decreasing in the gap compared to the pristine and depend on their position and the capacities of graphene in stabilize the imperfection. Content Type Journal Article Pages 207-217 DOI 10.3233/JCM-140497 Authors S. Dasilva, Laboratorio de Física de Metales, Departamento de Física, Escuela de Ciencias, Universidad de Oriente, Cumaná, Venezuela R. López-Planes, Laboratorio de Física de Metales, Departamento de Física, Escuela de Ciencias, Universidad de Oriente, Cumaná, Venezuela R. Carreño, Laboratorio de Física de Metales, Departamento de Física, Escuela de Ciencias, Universidad de Oriente, Cumaná, Venezuela E. Franco, Laboratorio de Física de Metales, Departamento de Física, Escuela de Ciencias, Universidad de Oriente, Cumaná, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: The elimination kinetics study of 2,4-dimethyl-2,4-pentanediol in gas phase at 440°C has been carried out using ab initio MP2 method with 6-31G, 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-311G(d) and 6-311G(d,p) basis functions set to explore the possibility of determining a possible concerted process with a six-membered cyclic transition state (TS). Vibrational frequencies analysis was realized in order to confirm the reactant, TS and products structures. The nature of these chemical species is examined in terms of geometrical parameters and of the charge density on the TQAIM analysis. IRC calculations have been performed in order to verify that localized TS structure connect with the corresponding minimum stationary points of the reactant and products. With the aim of corroborating the reaction mechanics postulated by Chuchani et al. [1] in their experimental work, we present a theoretical study in order to calculate the rate constant and the activation parameters. Results from MP2/6-311G(d,p) method was found to be in better agreement with the experimental values of the A-factor Arrhenius, activation energy and, activation enthalpy. However, at these levels of theory, it was not possible to reproduce the experimental values of the rate constant and, activation entropy. Content Type Journal Article Pages 195-205 DOI 10.3233/JCM-140496 Authors E. Echeverría, Lab de Química Computacional, Dpto de Química, Facultad de Ciencias y Tecnología, Universidad de Carabobo, Valencia, Venezuela J.A. Guaregua, Lab de Química Computacional, Dpto de Química, Facultad de Ciencias y Tecnología, Universidad de Carabobo, Valencia, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: The effect of the pre-adsorption of sulfur on the hexagonal-Mo_{2}C-(001) surface in the hydrodechlorination (HDC) reaction of chlorobenzene was studied using density functional theory (DFT) calculations. The results related with the coordination modes and the adsorption energies of the aromatic molecule suggest that the main effect of the sulfur incorporation into the surface is to lead towards a weaker chlorobenzene adsorption that will benefit the continuity of the catalytic cycle and therefore to avoid the carbonization and chlorination of the catalyst. The study of the HDC mechanism was also performed and two different reaction paths were considered. The calculated energy barriers indicate that both mechanisms may occur at the normal reaction temperature (350°C). These latter approaches involve new roles of the superficial sulfur as atomic or radical hydrogen scavenger for the S-Hformation and as a precursor of the σ chlorobenzene coordination, necessary for effective hydrogenation in the proposed mechanisms. Content Type Journal Article Pages 169-177 DOI 10.3233/JCM-140494 Authors Milagros Velásquez, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Alba B. Vidal, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Anelisse Bastardo, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Raquel del Toro, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Jesús Rodríguez, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Rafael Añez, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Paulino Betancourt, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Joaquín Brito, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Yosslen Aray, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela David S. Coll, Instituto Venezolano de Investigaciones Científicas,Centro de Química, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: This paper deals with the problem of evaluating the predictive and extrapolative ability of QSPR models by using the PaDEL-descriptor software. In this sense, the selections of training and external data sets were modified considering the molecular weight. Two criteria were used to evaluate the extapolative ability: high correlation factor (R^{2}) (criterion I) and positive ΔR^{2} and high R^{2} (criterion II). Based on internal and external validation, it is shown that criterion II has a better performance than criterion I. Other selection criteria were found by considering the maximum square correlation coefficient (Q_{ext}^2) or the minimum standard deviation (σ_{ext}) for the external set with high R^{2} values. These facts are supported by a systematic variation of the correlation factor (VCF) and the variation of correlation coefficients (VCC), as analysis tools proposed in this article. The methodology was successfully applied to critical temperature (Tc) estimation of linear alkanes and aromatic compounds, considering extrapolation to the heaviest compounds. Descriptors obtained for studied cases, using the criterion II, are in some way in agreement with group contribution and QSPR methods from literature. Content Type Journal Article Pages 155-167 DOI 10.3233/JCM-140493 Authors Alexander R. Peraza, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Laura Rojas, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Carín Bolívar, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Fernando Ruette, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: The objective of this contribution was to explore the effect of thermodynamic model selection on predicting the solubility of hydrogen in Pyrolysis Gasoline (PYGAS). In order to do this, different combinations of cubic equations of state (EOS), cohesion functions and mixing rules were compared, using both own algorithms and those implemented in the PRO/II 8.0 process simulation software. The models were selected following the recommendations made by some authors for H_{2} + hydrocarbons systems similar to the studied here. The cubic EOS of Redlich-Kwong (RK) and Peng-Robinson (PR) were considered using: five different cohesion functions, and the classical quadratic mixing rule (CQMR) with five single correlations to estimate the binary interaction parameters (BIP). Additionally, the system was simulated with PRO/II employing the Panagiotopoulos-Reid Modified (PA-RE-Mod) and the modified PA-RE mixing rule implemented by SimSci. The results were validated with experimental data reported in the literature for four temperatures 298 K, 313 K, 323 K, 343 K and pressures up to 6 MPa. The model composed by the RK EOS, Soave (1993) cohesion function, the CQMR with the BIP calculated with the Gray et al. correlation is the recommended selection to predict the solubility of H_{2} in PYGAS, under the considered conditions, with a 3.1% AARD (average absolute relative deviation). Content Type Journal Article Pages 137-153 DOI 10.3233/JCM-140492 Authors Mixef Rojas, Coordinación de Ingeniería Química, Universidad Simón Bolívar, Caracas, Venezuela Freddy Figueira, Grupo TADiP, Departamento de Termodinámica y Fenómenos de Transferencia, Universidad Simón Bolívar, Caracas, Venezuela Susana Zeppieri, Grupo de Fenómenos de Transporte GFT-10, Departamento de Termodinámica y Fenómenos de Transferencia, Universidad Simón Bolívar, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: Content Type Journal Article Category Editorial Pages 1-2 DOI 10.3233/JCM-140499 Authors Fernando Ruette, Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela Anibal Sierralta, Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela Morella Sánchez, Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: Quantum chemistry calculations were done, using the ONIOM2 methodology at two different levels of calculation, B3LYP for the high level and UFF for the low level. These calculations were performed on Au_{5}/SAPO-11, Au_{6}/SAPO-11, CO-Au_{5}/SAPO-11 and CO-Au_{6}/SAPO-11 aggregates to analyze the geometries of small clusters of Au_{5} and Au_{6} on SAPO-11 support. Au_{5} cluster presents a pentagonal structure in Au_{5}/SAPO-11. Au_{6} aggregate shows a "multi triangular" structure (as from a trapezoidal "W shaped" Au_{5}) in Au_{6}/SAPO-11. Au_{5} is also obtained as an "X shaped" structure. Similarly another Au_{6} aggregate configuration is obtained also multi triangular but as from X shape Au_{5} cluster. The CO interaction with Au_{5} and Au_{6}/SAPO-11 is studied. The formation energy ΔE_{F} of the aggregates, the CO adsorption energy ΔE_{ads} on them and CO frequency are presented. Content Type Journal Article Pages 45-52 DOI 10.3233/JCM-130483 Authors Beulah Griffe, Labs. Química Computacional y Fisicoquímica de Superficies, Centro de Química, IVIC, Caracas, Venezuela Joaquín L. Brito, Labs. Química Computacional y Fisicoquímica de Superficies, Centro de Química, IVIC, Caracas, Venezuela Anibal Sierraalta, Labs. Química Computacional y Fisicoquímica de Superficies, Centro de Química, IVIC, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: In this paper we study the manifestations of cooperative effects in the formation of supramolecular synthons observed in some thiohydantoin derivatives crystals. Energetic and structural properties were analyzed from the fully optimized clusters employing a DFT/B3LYP level of calculations, which reproduce the main features of the stereochemistry and geometries of the synthons exhibited by reported crystalline structures. The calculations performed in this work have also evidenced that the cluster stabilization is mainly due to the existence of strong cooperative effects, which display energetic as well as geometrical manifestations. The stabilization energy and stabilization energy per monomer, that comprises all the intermolecular interactions between the individual molecules that form the clusters, were computed, showing that the supramolecular clusters of 5-sec-butyl-2-tioxoimidazolidin-4-one is less stable than the compound 5-isopropyl-2-tioxoimidazolidin-4-one by 1.16 Kcal/mol. Finally, through this work it has been also evidenced the need of employing large basis sets, including polarization and diffuse effects, in order to properly model all the interactions existing in systems bonded by weak interactions. Content Type Journal Article Pages 5-16 DOI 10.3233/JCM-140480 Authors Luis E. Seijas, Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela Rafael Almeida, Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela Asiloé J. Mora, Laboratorio de Cristalografía, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela Gerzon E. Delgado, Laboratorio de Cristalografía, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: The additament of an impurity to a metal matrix generates a shift in the local electron density of states due to a change in the local electric potential so that an electron or electron beam will be scattered upon interaction with the ensuing potential, causing its wave function measured at a distance far removed from the source to show a quantum phase change. This phenomenon, reflected in Friedel's law, permits to relate the quantum phase shifts with both the density of states at the Fermi level and the transport properties of the system. This work calculates the electric resistivity of nanometric clusters in an aluminiumsupercell, emulating the formation of Guinier-Preston zones during pre-precipitation in an Al-Zn alloy. The density of states is evaluated each time a new atom of solute is added to the Al supercell using the ab initio method of the Density Functional Theory or DFT in its GGA and LDA approximations via the Dmol^{3} package of Materials Studio Software. A resistivity anomaly is obtained when, in concordance with literature reports for diluted AlZn alloys, the supercell contains 25 atoms, thus confirming that the electric resistivity anomaly during cluster formation is a consequence of both density of states variations and quantum transitions at the Fermi Level for a nanometric size in particular. The results are contrasted with those obtained via the transport equation. Content Type Journal Article Pages 29-43 DOI 10.3233/JCM-140482 Authors Diego Subero, Grupo Física de Metales, Dpto de Física, Núcleo de Sucre Cumaná, Universidad de Oriente, Venezuela Ney Luiggi, Grupo Física de Metales, Dpto de Física, Núcleo de Sucre Cumaná, Universidad de Oriente, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: A three-phase fixed-bed reactor for selective hydrogenation of butadiene in liquid phase with toluene as solvent is modeled using published kinetics. Thermodynamic and transport properties are estimated from models and correlations available in the literature. The model incorporates momentum and energy balances and mass transfer resistances. The results show that use of toluene increases the yield of cis-butane and trans-butane isomers by comparison with a previous study by Bressa et al. where a solvent was not included. The effects of temperature, pressure, hydrogen/butadiene ratio and toluene/feed ratio on the reactor performance are studied. A temperature rise of 37.8 K and a pressure drop of 100 kPa are predicted for a reactor 1 m in length and 0.58 m in diameter using a typical feed composition. Greater reactor lengths result in complete vaporization of the reacting mixture. This vaporization effect can be controlled by increasing the inlet pressure and toluene/feed ratio, and by decreasing the inlet temperature and hydrogen/butadiene ratio. The effect of inlet hydrogen/butadiene ratio is found to be negligible, whereas a rise in inlet temperature rise has a significant effect on the conversions and yields for the same reactor length. Finally, it was found that the yield of 1-butene increases with increasing inlet solvent/feed ratio and pressure. Content Type Journal Article Pages 103-119 DOI 10.3233/JCM-140488 Authors D.E. Pérez Vilela, Thermodynamics and Transport Phenomena Department, Simón Bolívar University, Caracas, Venezuela C. Olivera Fuentes, Thermodynamics and Transport Phenomena Department, Simón Bolívar University, Caracas, Venezuela S. Curbelo, Thermodynamics and Transport Phenomena Department, Simón Bolívar University, Caracas, Venezuela M.J. Rodríguez, Thermodynamics and Transport Phenomena Department, Simón Bolívar University, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: This paper implements a digital algorithm that allows the segmentation and skeletonization of digital images, this method is particularly important in the processing of retinographies where fundus analysis enables early detection of diseases such as diabetic retinopathy. The algorithm implemented using the Fourier transforms of two-dimensional Gabor and with the aid of conventional filters. The performance of the algorithm implemented under the Matlab mathematical platform has been compared with conventional methods resulting in obtaining filtered images with better contrast and higher resolution. Content Type Journal Article Pages 219-225 DOI 10.3233/JCM-140498 Authors Ronald Perez, Guajira University, Riohacha, Colombia William Lasso, Popular University of Cesar, Cesar, Colombia Carlos Jimenez, Applied Mathematics Group (GIMA), Guajira University, Riohacha, Colombia Lorenzo Mattos, Optics and Informatics Group (LOI), Popular University of Cesar, Cesar, Colombia Cesar O. Torres, Optics and Informatics Group (LOI), Popular University of Cesar, Cesar, Colombia Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: In this work, we study the interaction between OH radicals with black carbon (BC) modeled by a coronene molecule by means of quantum chemistry calculations MOPAC, DeMon-nano, DeMon2K packages with the purpose of understand the aging process of this material. Results show that strong OH radical adsorption is preferred on border sites than on center ones, independently of the theoretical method employed. Results of potential energy curves for OH adsorption show that a chemisorption state may occur with small barrier slower than 3.2 kcal/mol. At the center site a physisorbed state may take place. Once OH chemisorption happens, a dipole moment is created and the hydrophobic coronene surface is transformed to hydrophilic. For that reason water molecules are stabilized in the hydroxylated coronene surface by O^{…}H interactions. Chemisorption of many OH radicals, especially at edge sites, produces coronene hydroxylation that after subsequent OH attacks would lead to H abstractions directly from coronene and from chemisorbed OH. The last feature yield a C-C bond breaking at the coronene edge and the formation of hydroxyl and carboxylic groups. Both reactions were confirmed with DFT calculations using coordinates obtained by PM6. Small reaction barriers in both processes were found. From these preliminary results, it is concluded that a detailed modeling of OH interactions with a coronene molecule may shed some light in the formation of volatile oxygenate compounds and therefore the BC aging in the atmosphere. Content Type Journal Article Pages 81-91 DOI 10.3233/JCM-140486 Authors Laura Rojas, Laboratorio de Química Computacional, Centro de Química, IVIC, Caracas, Venezuela Tibisay Pérez, Laboratorio de Química Atmosférica, Centro de Química, IVIC, Caracas, Venezuela Loreto Donoso, Laboratorio de Química Atmosférica, Centro de Química, IVIC, Caracas, Venezuela Alexander Peraza, Laboratorio de Química Computacional, Centro de Química, IVIC, Caracas, Venezuela Fernando Ruette, Laboratorio de Química Computacional, Centro de Química, IVIC, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: The electronic properties of Al-Ti intermetallics are receiving great attention in the specialized literature because these alloys present excellent mechanical performance at high temperatures. This consideration prompted our DFT-LDA and DFT-GGA ab initio study on electronic band structures, density of states, contour plots, Fermi Surface, Bulk modulus, and cohesive energy of intermetallics Al_{3}Ti, AlTi, and AlTi_{3} using the FP-LAPW method. The band structure confirms their electrical conductivity, AlTi_{3} featuring a highly localized band associated to Ti 3d electrons around the Fermi level, not observed in the others. The DOS around the Fermi level is dominated by interactions between Al 3p and Ti 3d orbitals, whereas Al 3s and Ti 3d orbital interactions prevail in the regions of low and high energies, respectively. The density pseudogap in AlTi_{3} is located very close to the Fermi Level, granting a greater structural stability to this system. The Fermi Surface of these intermetallics, for which the authors found no previous reference in the literature, is reported. The difference in density distribution for the LDA and GGA methods is reflected in the contour plots. The Bulk modulus and cohesive energy values reported are in agreement with those reported in the literature. Content Type Journal Article Pages 53-71 DOI 10.3233/JCM-130484 Authors F. Pabel J. Machado, Grupo de Física de Metales, Dpto. de Física, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Venezuela. E-mail: p.j.001@hotmail.com, nluiggi51@gmail.com Ney Luiggi A., Grupo de Física de Metales, Dpto. de Física, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Venezuela. E-mail: p.j.001@hotmail.com, nluiggi51@gmail.com Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: We theoretically study the impact of an external noise on a kinetic mean-field model for the bistable catalytic CO oxidation on Pd(111) surfaces. A spatially homogeneous Gaussian white noise is imposed on the fraction of CO in the constant gas flow directed at the surface and the resulting stochastic system is analyzed by a set of Langevin equations. Using an adiabatic elimination technique, we are able to analyze the interplay between the noise and the kinetic bistability reported for this surface reaction in recent experimental studies. The analytical results predict a strong impact on the bistability phase diagram. The stochastic effects are analyzed by computing stationary solutions of the probability distribution functions and the transition times between the active and inactive states of the bistable region. We also introduce an effective potential description that allows us to analyze the impact of noise. Content Type Journal Article Pages 17-28 DOI 10.3233/JCM-130481 Authors Miguel Pineda, Department of Physics, Universidad Simón Bolívar, Caracas, Venezuela Raúl Toral, Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, Spain Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: We apply kinetic Monte Carlo simulations to study the catalytic oxidation of CO on a surface in the presence of contaminants in the gas phase. The dynamic behavior of the process is simulated by models based on the Ziff-Gulari-Barshad model (ZGB). We analyze three ways in which the entrance mechanism of the oxygen atoms can be modified such that the unphysical oxygen poisoned phase that characterizes the ZGB model disappears. We study the behavior of these models in the presence of impurities in the gas phase. Once on the surface, the impurities cannot be desorbed and do not react. We calculate the phase diagrams of the three cases for different percentages of impurities and study the behavior of the CO_2 production. We found that the non-desorbing impurities have the effect of eliminating the discontinuous phase transition to a CO poisoned phase, and that in the steady state there is no production of CO_2. However in the transient phase there can be an important CO_2 production that depends on the model. Content Type Journal Article Pages 73-80 DOI 10.3233/JCM-140485 Authors G.M. Buendía, Department of Physics, Universidad Simón Bolívar, Caracas, Venezuela G.A. Elcure, Department of Physics, Universidad Simón Bolívar, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: A detailed study of the interactions leading to stabilization of the NH_{3}(H_{2}O)_{n =1,2} clusters is presented in this work. The Potential Energy Surface for the trimers was explored using an adapted version of the simulated annealing optimization procedure that produced cluster candidate structures that were further optimized, refined, and characterized at the MP2/6–311++G(d, p) level. Our results indicate that hydrogen bonding of the N…H type is stronger and more covalent than of the O…H type. We provide evidence that suggests that the topological complexity of the electron distributions is directly correlated with cluster stability and that most of the stabilization energy originates in electrostatic and exchange contributions. Our calculated trimerization enthalpy, ΔH^°_{298} −41.75 kJ/mol, is in excellent agreement with the experimental enthalpy of adsorption of NH_{3} into surface water, reported to be − (41 ± 5) kJ/mol. Content Type Journal Article Pages 93-102 DOI 10.3233/JCM-140487 Authors Doris Guerra, Grupo de Química – Física Teórica, Instituto de Química, Universidad de Antioquia, Medellín, Colombia Jorge David, Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, Medellín, Colombia Albeiro Restrepo, Grupo de Química – Física Teórica, Instituto de Química, Universidad de Antioquia, Medellín, Colombia Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: In this study, we carried out two-layer ONIOM(DFT:MM) calculations to determine the adsorption enthalpies and vibrational frequencies of NO and CO molecules, on palladium exchanged zeolite (Pd/ZSM-5) catalyst. The results reveal that the local Al distribution near to Pd^{+2} influence the stretching frequencies as well as the adsorption enthalpies. The nine possible Al distributions studied can be gathered in two groups. One responsible for high CO and NO frequencies (ε_{CO}= 2146 cm^{-1} and ε_{NO}= 1880 cm^{-1}) and the other one responsible for the low frequencies (ε_{CO} = 2127 cm^{-1} and ε_{NO}= 1840 cm^{-1}). In general, the adsorption enthalpy of the CO is similar to the NO therefore; there is not a preferential adsorption of CO over the NO molecule. Content Type Journal Article Pages 121-130 DOI 10.3233/JCM-140490 Authors Anibal Sierraalta, Laboratorio de Química Computacional, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Rafael Añez, Laboratorio de Química Computacional, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Dianela Rincón, Laboratorio de Química Computacional, Centro de Química, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: In this paper we introduce AIM-UC, a free application that allows to create graphs related to Quantum Theory of Atoms in Molecules (QTAIM). The input data are files that contain 3D grid of electron density, in some known formats: CUBE from gaussian, grd from DMol and CHGCAR from VASP. Also it supports wave function files from AIMPAC. The application calculates 2D regular grids (electron densities and its laplacians) in a plane positioned by the user. By using bicubic interpolation and the Newton-Raphson method, the critical points at the plane can be calculated, and the gradient field and molecular graph can also be generated using the Cash-Karp Runge-Kutta method. It also permits plotting the electron density and its negative laplacian on the selected plane. Moreover, for both 2D grids, it is possible to calculate the contour maps using the "Marching Squares" algorithm. This application also permits finding the critical points in the 3D space. The output consist of plain text files and images in PNG, BMP and EPS (encapsulated post script) formats. AIM-UC was programmed in C++, using the GUI toolkit FLTK (fast light toolkit) and OpenGL (open graphic library). Content Type Journal Article Pages 131-136 DOI 10.3233/JCM-140491 Authors D. Vega, Laboratorio de Química Computacional, FACYT, Universidad de Carabobo, Bárbula, Edo. Carabobo, Venezuela D. Almeida, Laboratorio de Química Computacional, FACYT, Universidad de Carabobo, Bárbula, Edo. Carabobo, Venezuela Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 1-3 / 2014

Description: In recent days, due to the rapid technological advancements, the grid computing has become an important area of research in distributed systems. The load balancing is a very important and complex problem in grid computing. In this paper, we propose a dynamic-distributed load-balancing technique called the improved load balancing on enhanced GridSim with deadline control (IEGDC) for computational grids. Here, we provide a new mechanism of scheduling to enhance the utilization of the resources and to prevent the resource overloading. A selection method for scheduling by considering the state of resource bandwidth and capacity of various resources is presented. We simulate the proposed load-balancing strategy on the GridSim platform. The proposed mechanism on comparison is found to outperform the existing schemes in terms of response time, resubmitted time, finished and unfinished Gridlets. The simulation results are presented.

Description: Virtual bioactive molecular design is an important part of modern drug discovery projects. In this regard, molecular docking may be looked upon as a well established in silico approach in structure-based hit/lead development. Stereoelectronic complementary fit of a bioactive ligand with its receptor may be predicted by molecular docking. Generally docking simulations are compromised of two principal steps; search algorithm and a scoring function. Search algorithms explore the ligand-receptor configurational space while scoring functions apply molecular mechanic force fields to estimate the free binding energies of various ligand-enzyme poses. In the present contribution, a new probability factor (PF) was proposed that could successfully enhance the predictability of AutoDock4.2 scoring function with regard to FRET-based BACE-1 inhibitory activities of some organic small molecules. BACE-1 or beta site amyloid precursor protein cleaving enzyme is a major therapeutic target for Alzheimer disease due to its determinant role in pathogenesis of the disease. Content Type Journal Article Pages 315-325 DOI 10.3233/JCM-140506 Authors Nima Razzaghi-Asl, Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran Bahram Hemmateenejad, Chemistry Department, Shiraz University, Shiraz, Iran Ahmad Ebadi, Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran Sara Shahabipour, Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran Ramin Miri, Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: The main goal of this article is to demonstrate the use of the Reduced Differential Transform Method (RDTM). This method has been applied directly without using bilinear forms, Wronskian, or inverse scattering method. Also it is worth pointing out that if the terms of the series increase, the RDTM provides better convergence to the analytical solution. In this paper, this method is used for solving nonlinear coupled MKdV equation with given initial conditions having arbitrary constants. The numerical solutions obtained by RDTM are compared with the known exact solutions by fixing the arbitrary constants and with Adomian Decomposition Method (ADM) in tables as well as in figures. Content Type Journal Article Pages 269-275 DOI 10.3233/JCM-140504 Authors Amit Tomar, Department of Mathematics, DIT University, Dehradun, India Rajan Arora, Department of Applied Science and Engineering, Indian Institute of Technology Roorkee, India Journal Journal of Computational Methods in Science and Engineering Online ISSN 1875-8983 Print ISSN 1472-7978 Journal Volume Volume 14 Journal Issue Volume 14, Number 4-5 / 2014

Description: This article addresses the problem of NURBS surface deformation design using surface feature transplantation. To represent the semantic surface feature, a new surface feature representation called normal feature membrane is proposed. In the proposed method, the base surfaces of the source surface with the feature that the designer is highly interested in and the target surface to be deformed are first constructed. This is followed by extracting the normal feature membrane of the source surface. The deformation design is then realized by transplanting the extracted normal feature membrane of the source surface to the base surface of the target surface through four main operations, which are normal feature membrane preprocessing, normal feature membrane transplanting, surface fairing, and boundary feature decaying, respectively. The proposed method provides an easy copy–paste operation of the semantic surface feature for surface deformation of complex product. The examples of the surface feature transplantation for the surface design of automobile bodies are given to verify the validity and feasibility of the proposed method.

Description: Backbreak is one of the undesirable effects of blasting operations causing instability in mine walls, falling down the machinery, improper fragmentation and reduction in efficiency of drilling. Backbreak can be affected by various parameters such as the rock mass properties, blasting geometry and explosive properties. In this study, the application of the artificial neural network (ANN), an adaptive neuro-fuzzy inference system (ANFIS) for prediction of backbreak, was described and compared with the traditional statistical model of multiple regression. The performance of these models was assessed through the root mean square error, correlation coefficient ( R 2 ) and mean absolute percentage error. As a result, it was found that the constructed ANFIS exhibited a higher performance than the ANN and multiple regression for backbreak prediction.

Description: We present a parametric model for generating unit cells with randomly distributed inclusions. The proposed algorithm possesses (1) robustness by yielding unit cells with fiber volume fraction of up to 45 % for aspect ratios as high as 20, (2) computationally efficiency accomplished through a hierarchy of algorithms with increasing computational complexity, and (3) versatility by generating unit cells with different inclusion shapes. A statistical study aimed at determining the effective size of the unit cell is conducted. The method has been applied to various random inclusion microstructure composites, including: (1) two-dimensional chopped tow composites employed in automotive applications, (2) polyurea or polyethene coating consisting of hard and soft domains (segments) employed for energy absorption in military and industrial applications, and (3) fiber framework called fiberform embedded in or free from an amorphous matrix used as heat shield on space crafts to prevent structural damage during reentry into the atmosphere.

Description: Integrating analysis and design models is a complex task due to differences between the models and the architectures of the toolsets used to create them. This complexity is increased with the use of many different tools for specific tasks during an analysis process. In this work various design and analysis models are linked throughout the design lifecycle, allowing them to be moved between packages in a way not currently available. Three technologies named Cellular Modeling, Virtual Topology and Equivalencing are combined to demonstrate how different finite element meshes generated on abstract analysis geometries can be linked to their original geometry. Cellular models allow interfaces between adjacent cells to be extracted and exploited to transfer analysis attributes such as mesh associativity or boundary conditions between equivalent model representations. Virtual Topology descriptions used for geometry clean-up operations are explicitly stored so they can be reused by downstream applications. Establishing the equivalence relationships between models enables analysts to utilize multiple packages for specialist tasks without worrying about compatibility issues or substantial rework.

Description: Grid-based methods for generating all-hex meshes show tremendous promise in automating and speeding up turnaround for computational simulations for solid mechanics. Recognizing some of the inherent weaknesses of grid-based methods, there has been hesitancy in accepting this technology as a viable option for critical FEA. The authors extend previous work on a grid-based method known as sculpt, and evaluate its effectiveness in practice. This study attempts to compare meshes generated with traditional manual pave-and-sweep technologies with those generated with sculpt’s automatic overlay grid method. We use a simple torsion pin analysis to understand both linear-elastic and non-linear elastic–plastic responses with grid-based meshes. We also introduce improvements to the sculpt grid-based procedure, including adaptive optimization-based smoothing, hex-dominant and pillowing to capture curve features as proposed techniques for improving mesh quality. This study demonstrates that in the cases tested, equivalent or superior results were achieved with grid-based meshes when compared to pave-and-sweep meshes.

Description: The modern engineering design process often relies on numerical analysis codes to evaluate candidate designs, a setup which formulates an optimization problem which involves a computationally expensive black-box function. Such problems are often solved using a algorithm in which a metamodel approximates the true objective function and provides predicted objective values at a lower computational cost. The metamodel is trained using an initial sample of vectors, and this implies that the procedure by which the initial sample is generated can impact the overall effectiveness of the optimization search. Approaches for generating the initial sample include the statistically based design of experiments, and the more recent search-driven sampling which generates the sample vectors with a direct-search optimizer. This study compares these two approaches in terms of their overall impact on the optimization search and formulates guidelines in which scenario is each approach preferable. An extensive analysis shows that: (a) the main factor affecting search-driven sampling is the size of the initial sample, and such methods performed better in large initial samples, (b) design of experiments methods tended to perform better in lower sample sizes, (c) generating a sample which is space-filling improved the overall search effectiveness

Description: The sweeping algorithm is one of the most robust techniques to generate hexahedral meshes. During one-to-one sweeping, the most difficult thing is to map an all-quad source surface mesh onto its target surface. In this paper, a harmonic function is used to map meshes from a source surface to its target surface. The result shows that it can generate an all-quad mesh on the target surface with good mesh quality for the convex, concave or multiply-connected surface and thus avoid expensive smoothing algorithm (untangling). Meanwhile, the cage-based deformation method is used to locate interior nodes between the source and target surface during sweeping. Finally, examples are provided and the execution time for our proposed algorithm is discussed.

Description: This paper describes an overset approach that comprised virtual boundary-layer -like near-body grid coupled with an off-body adaptive mesh refinement far-field mesh for viscous fluids simulations. Unlike most a priori grid generation systems for the Reynolds-Averaged Navier–Stokes equations, the strand meshing paradigm is automatic, fast and requires little memory to provide boundary-layer coverage. In addition, the stacks of elements implied by the strands can be used to the simulation’s advantage, where they naturally provide a line direction for semi-implicit solving.

Description: This work recovers an established technique for improving quadrilateral shell element performance in both out-of-plane and in-plane bending cases using a mixed formulation. A four-field variational principle is established and we relate, at the discrete level, the Lagrange multipliers and secondary right Cauchy–Green field with the displacement and rotation fields. This is the main contribution of this work. High coarse-mesh accuracy is observed for distorted meshes and the robustness is shown to be adequate for crack propagation simulations. A consistent director normalization is performed, as an alternative to our recent spherical interpolation. Covariant metric components are deduced and exact linearization of the shell element is performed. Full assessment of the element is accomplished, showing similar performance to more costly approaches such as enhanced assumed strain. Patch test is satisfied ab-initio and benchmarks present very accurate results. Numerical experimentation for geometrically and material nonlinear problems is presented, as well as one fracture example using our recently proposed cracked edge technique.

Description: This paper presents a method to compute accurate bounds on Jacobian determinants of high-order (curvilinear) triangular finite elements. This method can be used to guarantee that a curvilinear triangle is geometrically valid, i.e., its Jacobian determinant is strictly positive everywhere in its reference domain. It also provides an efficient way to measure the quality of triangles. The key feature of the method is to expand the Jacobian determinant using a polynomial basis, built using Bézier functions, that has both properties of boundedness and positivity. Numerical results show the sharpness of our estimates.

Description: In this work, we introduce a new method for generating Lagrangian computational meshes from Eulerian-based data. We focus specifically on shock physics problems that are relevant to Eulerian-based codes that generate volume fraction data on a Cartesian grid. A step-by-step procedure for generating an all-hexahedral mesh is presented. We focus specifically on the challenges of developing a parallel implementation using the message passing interface to ensure a continuous, conformal and good quality hex mesh.

Description: This paper introduces Voronoi squared distance minimization (VSDM), an algorithm that fits a surface to an input mesh. VSDM minimizes an objective function that corresponds to a Voronoi-based approximation of the overall squared distance function between the surface and the input mesh (SDM). This objective function is a generalization of the one minimized by centroidal Voronoi tessellation, and can be minimized by a quasi-Newton solver. VSDM naturally adapts the orientation of the mesh elements to best approximate the input, without estimating any differential quantities. Therefore, it can be applied to triangle soups or surfaces with degenerate triangles, topological noise and sharp features. Applications of fitting quad meshes and polynomial surfaces to input triangular meshes are demonstrated.

Description: Solving partial differential equations using finite element (FE) methods for unstructured meshes that contain billions of elements is computationally a very challenging task. While parallel implementations can deliver a solution in a reasonable amount of time, they suffer from low cache utilization due to unstructured data access patterns. In this work, we reorder the way the mesh vertices and elements are stored in memory using Hilbert space-filling curves to improve cache utilization in FE methods for unstructured meshes. This reordering technique enumerates the mesh elements such that parallel threads access shared vertices at different time intervals, reducing the time wasted waiting to acquire locks guarding atomic regions. Further, when the linear system resulting from the FE analysis is solved using the preconditioned conjugate gradient method, the performance of the block-Jacobi preconditioner also improves, as more nonzeros are present near the stiffness matrix diagonal. Our results show that our reordering reduces the L1 and L2 cache miss-rates in the stiffness matrix assembly step by about 50 and 10 %, respectively, on a single-core processor. We also reduce the number of iterations required to solve the linear system by about 5 %. Overall, our reordering reduces the time to assemble the stiffness matrix and to solve the linear system on a 4-socket, 48-core multi-processor by about 20 %.

Description: The development of parallel algorithms for mesh generation, untangling, and quality improvement is of high importance due to the need for large meshes with millions to billions of elements and the availability of supercomputers with hundreds to thousands of cores. There have been prior efforts in the development of parallel algorithms for mesh generation and local mesh quality improvement in which only one vertex is moved at a time. But for global mesh untangling and for global mesh quality improvement, where all vertices are simultaneously moved, parallel algorithms have not yet been developed. In our earlier work, we developed a serial global mesh optimization algorithm and used it to perform mesh untangling and mesh quality improvement. Our algorithm moved the vertices simultaneously to optimize a log-barrier objective function that was designed to untangle meshes as well as to improve the quality of the worst quality mesh elements. In this paper, we extend our work and develop a parallel log-barrier mesh untangling and mesh quality improvement algorithm for distributed-memory machines. We have used the algorithm with an edge coloring-based algorithm for synchronizing unstructured communication among the processes executing the log-barrier mesh optimization algorithm. The main contribution of this paper is a generic scheme for global mesh optimization, whereby the gradient of the objective function with respect to the position of some of the vertices is communicated among all processes in every iteration. The algorithm was implemented using the OpenMPI 2.0 parallel programming constructs and shows greater strong scaling efficiency compared to an existing parallel mesh quality improvement technique.

Description: We present different linear parametrization techniques for the purpose of surface remeshing: the energy minimizing harmonic map, the convex map, and the least square conformal map. The implementation of those mappings as well as the associated boundary conditions is presented in a unified manner and the issues of triangle flipping and folding that may arise with discrete linear mappings are discussed. We explore the optimality of these parametrizations for surface remeshing by applying several classical 2D meshing algorithms in the parametric space and by comparing the quality of the generated elements. We present various examples that permit to draw guidelines that a user can follow in choosing the best parametrization scheme for a specific topology, geometry, and characteristics of the target output mesh.

Description: We present a new method to construct a trivariate T-spline representation of complex solids for the application of isogeometric analysis. We take a genus-zero solid as a basis of our study, but at the end of the work we explain the way to generalize the results to any genus solids. The proposed technique only demands a surface triangulation of the solid as input data. The key of this method lies in obtaining a volumetric parameterization between the solid and the parametric domain, the unitary cube. To do that, an adaptive tetrahedral mesh of the parametric domain is isomorphically transformed onto the solid by applying a mesh untangling and smoothing procedure. The control points of the trivariate T-spline are calculated by imposing the interpolation conditions on points sited both on the inner and on the surface of the solid. The distribution of the interpolating points is adapted to the singularities of the domain to preserve the features of the surface triangulation. We present some results of the application of isogeometric analysis with T-splines to the resolution of Poisson equation in solids parameterized with this technique.

Description: This paper presents a method for detecting holes during the surface wrapping process which cause surface leaks into the volume parts that shall not be meshed. The method solves a heat-diffusion equation on the background octree mesh, which is generated based on user-defined parameters, and its resolution corresponds to the resolution of the wrapper surface mesh. The heat problem is posed with the constant heat source in the volume, and the holes are detected as regions of high temperature gradients. The method detects both holes with open-boundary edges and semantic holes due to some missing parts. The sensitivity of the method is controlled via user-adjustable parameter which represents the ratio between the volume that shall not be meshed and the area of the hole. In addition, it is demonstrated that the method can be used to correct the orientation of normals in the surface mesh by utilising the property that high temperature is always found inside the volume. The potential of the method is presented on complex engineering examples.

Description: In this paper, a novel approach to automatically sub-divide a complex geometry and apply an efficient mesh is presented. Following the identification and removal of thin-sheet regions from an arbitrary solid using the thick/thin decomposition approach developed by Robinson et al. [ 1 ], the technique here employs shape metrics generated using local sizing measures to identify long-slender regions within the thick body. A series of algorithms automatically partition the thick region into a non-manifold assembly of long-slender and complex sub-regions. A structured anisotropic mesh is applied to the thin-sheet and long-slender bodies, and the remaining complex bodies are filled with unstructured isotropic tetrahedra. The resulting semi-structured mesh possesses significantly fewer degrees of freedom than the equivalent unstructured mesh, demonstrating the effectiveness of the approach. The accuracy of the efficient meshes generated for a complex geometry is verified via a study that compares the results of a modal analysis with the results of an equivalent analysis on a dense tetrahedral mesh.

Description: The presence of a few inverted or poor-quality mesh elements can negatively affect the stability, convergence and efficiency of a finite element solver and the accuracy of the associated partial differential equation solution. We propose a mesh quality improvement and untangling method that untangles a mesh with inverted elements and improves its quality. Worst element mesh quality improvement and untangling can be formulated as a nonsmooth unconstrained optimization problem, which can be reformulated as a smooth constrained optimization problem. Our technique solves the latter problem using a log-barrier interior point method and uses the gradient of the objective function to efficiently converge to a stationary point. The method uses a logarithmic barrier function and performs global mesh quality improvement. We have also developed a smooth quality metric that takes both signed area and the shape of an element into account. This quality metric assigns a negative value to an inverted element. It is used with our algorithm to untangle a mesh by improving the quality of an inverted element to a positive value. Our method usually yields better quality meshes than existing methods for improvement of the worst quality elements, such as the active set, pattern search, and multidirectional search mesh quality improvement methods. Our method is faster and more robust than existing methods for mesh untangling, such as the iterative stiffening method.

Description: A procedure to quantify the distortion (quality) of a high-order mesh composed of curved tetrahedral elements is presented. The proposed technique has two main applications. First, it can be used to check the validity and quality of a high-order tetrahedral mesh. Second, it allows the generation of curved meshes composed of valid and high-quality high-order tetrahedral elements. To this end, we describe a method to smooth and untangle high-order tetrahedral meshes simultaneously by minimizing the proposed mesh distortion. Moreover, we present a \(p\) -continuation procedure to improve the initial configuration of a high-order mesh for the optimization process. Finally, we present several results to illustrate the two main applications of the proposed technique.

Description: The generation of meshes that correctly reproduce a prescribed size function is crucial for quadrilateral meshing due to two reasons. First, quadrilateral meshes are difficult to adapt to a given size field by refining or coarsening the elements without compromising the element quality. Second, after the meshing algorithm is finished, it may be necessary to apply a smoothing algorithm to improve the global quality. This smoothing step may modify the element size and the final mesh will not reproduce the prescribed element size. To solve these issues, we propose to combine the size-preserving method with a smoothing technique that takes into account both the element shape and size. The size-preserving technique allows directly generating a quadrilateral mesh that reproduces the size function, while the proposed smoother allows obtaining a high-quality mesh while maintaining the element size. In adaptive processes, the proposed approach may reduce the number of iterations to achieve convergence, since at each iteration the background mesh is properly reproduced. In addition, we detail new theoretical results that provide more insight to size-preserving size functions. Specifically, we prove that the maximum gradient of a one-dimensional size-preserving size function is bounded. Finally, several applications that show the benefits of applying the proposed techniques are presented.

Description: In this paper compute unified device architecture programming and open multiprocessing are used for the graphics processing unit and central processing unit parallel computation of material damage. The material damage is evaluated by a multilevel finite element analysis within material domains reconstructed from a high-resolution micro-focus X-ray computed tomography system. An effective computational method is investigated for solving the linear equations of finite element analysis. Numerical results show an encouraging trend in reducing the computation cost for the digital diagnosis of material damage.

Description: This paper presents a novel algorithm that enables the semi-automatic reconstruction of human-made structures (e.g., buildings) into piecewise planar 3D models from a single image. This allows the models to be readily used in virtual or augmented reality visual simulations or for data acquisition in 3D geographic information systems. Contrary to traditional labor-intensive but accurate single view reconstruction (SVR) solutions based purely on geometric constraints, and contrary to recent fully automatic albeit low-accuracy SVR algorithms based on statistical inference, the presented method achieves a compromise between speed and accuracy, leading to less user input and acceptable visual effects. The user input required in the presented approach is primarily a line drawing that represents an outline of the building to be reconstructed. Using this input, the developed method takes advantage of a newly proposed vanishing point (VP) detection algorithm that can simultaneously estimate multiple VPs in an image. With those VPs, the normal direction of planes—which are projected onto the image plane as polygons in the line drawing—can be automatically calculated. Following this step, a linear system similar to the traditional SVR solutions can be used to achieve 3D reconstruction. Experiments that demonstrate the efficacy and visual outcome of the developed method are also described, highlighting the method’s potential use for rapid geometric model building of surrounding structures in visual simulation of engineering processes.

Description: Efficient development and engineering of high performing interactive devices, such as haptic robots for surgical training benefits from model-based and simulation-driven design. The complexity of the design space and the multi-domain and multi-physics character of the behavior of such a product ask for a systematic methodology for creating and validating compact and computationally efficient simulation models to be used in the design process. Modeling the quasi-static stiffness is an important first step before optimizing the mechanical structure, engineering the control system, and performing hardware in the loop tests. The stiffness depends not only on the stiffness of the links, but also on the contact stiffness in each joint. A fine-granular Finite element method (FEM) model, which is the most straightforward approach, cannot, due to the model size and simulation complexity, efficiently be used to address such tasks. In this work, a new methodology for creating an analytical and compact model of the quasi-static stiffness of a haptic device is proposed, which considers the stiffness of actuation systems, flexible links and passive joints. For the modeling of passive joints, a hertzian contact model is introduced for both spherical and universal joints, and a simply supported beam model for universal joints. The validation process is presented as a systematic guideline to evaluate the stiffness parameters both using parametric FEM modeling and physical experiments. Preloading has been used to consider the clearances and possible assembling errors during manufacturing. A modified JP Merlet kinematic structure is used to exemplify the modeling and validation methodology.