Tae-Hyuk Ahn¹, Layne T. Watson^1,2, Yang Cao^1,1, Clifford A. Shaffer¹, William T. Baumann³

CMES-Computer Modeling in Engineering & Sciences, Vol.51, No.1, pp. 27-52, 2009, DOI:10.3970/cmes.2009.051.027

Abstract For biochemical systems, where some chemical species are represented by small numbers of molecules, discrete and stochastic approaches are more appropriate than continuous and deterministic approaches. The continuous deterministic approach using ordinary differential equations is adequate for understanding the average behavior of cells, while the discrete stochastic approach accurately captures noisy events in the growth-division cycle. Since the emergence of the stochastic simulation algorithm (SSA) by Gillespie, alternative algorithms have been developed whose goal is to improve the computational efficiency of the SSA. This paper explains and empirically compares the performance of some of these SSA alternatives on a realistic… More >

M.J. Galán Moreno, J.J. Sánchez Medina, L. Álvarez Álvarez E. Rubio Royo¹

CMES-Computer Modeling in Engineering & Sciences, Vol.50, No.3, pp. 191-226, 2009, DOI:10.3970/cmes.2009.050.191

Abstract Urban traffic is a key factor for the development of a city. There exist many different approaches facing traffic optimization. In our case we have focused on traffic lights optimization. We have designed and tested a new architecture to optimize traffic light cycle times. The purpose of this research is to demonstrate the good performance of our architecture in a congested scenario. We have simulated several congestion situations for a very large real world traffic network - "La Almozara" in Zaragoza, Spain. Our results seem encouraging in this extreme situation. As we increase the load in the network we get… More >

D. Kourounis¹, L.N. Gergidis¹, A. Charalambopoulos¹

CMES-Computer Modeling in Engineering & Sciences, Vol.28, No.3, pp. 185-202, 2008, DOI:10.3970/cmes.2008.028.185

Abstract The sensitivity of analytical solutions of the direct acoustic scattering problem in prolate spheroidal geometry on the wavenumber and shape, is extensively investigated in this work. Using the well known Vekua transformation and the complete set of radiating "outwards'' eigensolutions of the Helmholtz equation, introduced in our previous work ([Charalambopoulos and Dassios(2002)], [Gergidis, Kourounis, Mavratzas, and Charalambopoulos (2007)]), the scattered field is expanded in terms of it, detouring so the standard spheroidal wave functions along with their inherent numerical deficiencies. An approach is employed for the determination of the expansion coefficients, which is optimal in the sense, that minimizes the… More >

RaviS Nanjundiah¹

CMES-Computer Modeling in Engineering & Sciences, Vol.27, No.1&2, pp. 1-24, 2008, DOI:10.3970/cmes.2008.027.001

Abstract In this paper, application of high performance computing to climate modelling with specific reference to global General Circulation Models (GCM) is discussed. Methods of parallelization of global atmospheric models based on their numerical schemes is presented. It is seen that there is an interesting co-evolution of computer architecture and the type of numerical schemes used in general circulation models. A detailed survey of the Indian HPC scenario for meteorological computing is presented. Innovative and pioneering aspects of Indian efforts are highlighted. More >

Chein-Shan Liu¹

CMES-Computer Modeling in Engineering & Sciences, Vol.26, No.3, pp. 157-168, 2008, DOI:10.3970/cmes.2008.026.157

Abstract For the Sturm-Liouville eigenvalues problem we construct a very effective Lie-group shooting method (LGSM) to search the eigenvalues, and when eigenvalue is determined we can also search a missing left-boundary condition of the slope through a weighting factor r ∈ (0,1). Hence, the eigenvalues and eigenfunctions can be calculated with a better accuracy. Because a closed-form formula is derived to calculate unknown slope in terms of λ for the estimation of eigenvalues, the present method is easy to implement and has a low computational cost. Similarly by applying the LGSM to find a corresponding eigenfunction in terms of λ is… More >

L.N. Gergidis, D. Kourounis, S. Mavratzas, A. Charalambopoulos¹

CMES-Computer Modeling in Engineering & Sciences, Vol.21, No.2, pp. 157-176, 2007, DOI:10.3970/cmes.2007.021.157

Abstract A new complete set of scattering eigensolutions of Helmholtz equation in spheroidal geometry is constructed in this paper. It is based on the extension to exterior boundary value problems of the well known Vekua transformation pair, which connects the kernels of Laplace and Helmholtz operators. The derivation of this set is purely analytic. It avoids the implication of the spheroidal wave functions along with their accompanying numerical deficiencies. Using this novel set of eigensolutions, we solve the acoustic scattering problem from a soft acoustic spheroidal scatterer, by expanding the scattered field in terms of it. Two approaches concerning the determination… More >

J. Ma¹, H. Lu¹, B. Wang¹, S. Roy¹, R. Hornung², A. Wissink², R. Komanduri^1,3

CMES-Computer Modeling in Engineering & Sciences, Vol.8, No.2, pp. 135-152, 2005, DOI:10.3970/cmes.2005.008.135

Abstract In the simulation of a wide range of mechanics problems including impact/contact/penetration and fracture, the material point method (MPM), Sulsky, Zhou and Shreyer (1995), demonstrated its computational capabilities. To resolve alternating stress sign and instability problems associated with conventional MPM, Bardenhagen and Kober (2004) introduced recently the generalized interpolation material point (GIMP) method and implemented for one-dimensional simulations. In this paper we have extended GIMP to 2D and applied to simulate simple tension and indentation problems. For simulations spanning multiple length scales, based on the continuum mechanics approach, we present a parallel GIMP computational method using the Structured Adaptive Mesh… More >

J. Bielak¹, O. Ghattas², E.-J. Kim³

CMES-Computer Modeling in Engineering & Sciences, Vol.10, No.2, pp. 99-112, 2005, DOI:10.3970/cmes.2005.010.099

Abstract We present a parallel octree-based finite element method for large-scale earthquake ground motion simulation in realistic basins. The octree representation combines the low memory per node and good cache performance of finite difference methods with the spatial adaptivity to local seismic wavelengths characteristic of unstructured finite element methods. Several tests are provided to verify the numerical performance of the method against Green's function solutions for homogeneous and piecewise homogeneous media, both with and without anelastic attenuation. A comparison is also provided against a finite difference code and an unstructured tetrahedral finite element code for a simulation of the 1994 Northridge… More >

Yu.A. Melnikov, M.Yu. Melnikov¹

CMES-Computer Modeling in Engineering & Sciences, Vol.2, No.2, pp. 291-306, 2001, DOI:10.3970/cmes.2001.002.291

Abstract The use of potential (integral) representations is studied when computing Green's functions for boundary value problems stated for Laplace and biharmonic equations over regions of complex configuration in two dimensions. The emphasis is on the non-traditional potentials, whose observation and source points occupy different sets. Such potentials reduce the original boundary value problems to functional (integral) equations with smooth kernels. Special integral representations are studied, the ones whose kernels are built not of the fundamental solutions of governing differential equations but of the Green's functions for simply shaped regions, which are associated with boundary value problems under consideration. Such integral… More >