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Turbulence has been modeled by a two equation k-ω turbulence model to investigate the wind induced circulation patterns in coastal waters. Predictions of the model have been compared by the predictions of two equation k-ε turbulence model. Kinetic energy of turbulence is k, dissipation rate of turbulence is ε, and frequency of turbulence is ω. In the three dimensional modeling of turbulence by k-ε...
Four widely-used techniques for vortex detection in turbulent flows are investigated and compared. The flow of a viscous incompressible fluid in a plane channel is simulated numerically by means of a parallel computational code based on a mixed spectral-finite difference algorithm for the numerical integration of the Navier-Stokes equations. The DNS approach (Direct Numerical Simulation) is followed...
A high-resolution semi-discrete central-upwind scheme for solving a two class Lighthill-Whitham-Richards (LWR) traffic flow model is investigated in this paper. This scheme is based on combining a fourth-order central weighted essentially nonoscillatory (CWENO) reconstruction with semi-discrete central-upwind numerical flux. The CWENO re construction is chosen to improve the accuracy and guarantee...
The simulation of fluid phenomena, such as smoke, water, fire, has developed rapidly in computer games, special effects, and animation. The various physics-based methods can result in high quality images. However, the simulation speed is also important issue for consideration in applications. This paper describes an efficient method for controlling smoke simulation, running entirely on the GPU. Our...
Efficient and robust nonlinear solvers, based on Variable Relaxation, is developed to solve nonlinear anisotropic thermal conduction arising from fusion plasma simulations. By adding first and/or second order time derivatives to the system, this type of methods advances corresponding time-dependent nonlinear systems to steady state, which is the solution to be sought. In this process, only the stiffness...
A numerical model has been developed for the simulation long wave propagation and run-up accounting for the bottom friction. Shallow water continuity and momentum equations are solved numerically by a two time step finite difference method. The upwind/downwind method is applied to the nonlinear advection terms and the continuity equation. Effects of damping and bottom friction on the computations...
The Southern California Earthquake Center initiated a major large-scale earthquake simulation called TeraShake. The simulations propagated seismic waves across a domain of 600x300x80 km at 200 meter resolution, some of the largest and most detailed earthquake simulations of the southern San Andreas fault. The output from a single simulation may be as large as 47 terabytes of data and 400,000 files...
This paper presents a new model for the computation of the insolation in large territories. The main novelty of this work consists in that it reduces significatively the number of necessary arithmetic operations, and simplifies the calculations introducing errors that are inferior to the ones imposed by the climate in a territory. In particular, a faster algorithm to compute the horizon at all points...
The subject of non-equilibrium thermodynamics is now quite old, dating back to Prigogine, Biot and Truesdell in the 1950’s and 1960’s. It has had a resurgence in the physical sciences in the past five years largely due to a consolidation of ideas on thermodynamics as a whole and to advances in computer speeds. Non-equilibrium thermodynamics has now advanced to a stage where it forms an umbrella approach...
A finite element model for epidermal wound healing is proposed. The model takes into account the sequential steps of angiogenesis (neo-vascularization) and wound contraction (the actual healing of a wound). An innovation in the present study is the combination of both partially overlapping processes, yielding novel insights into the process of wound healing. The models consist of nonlinearly coupled...
Hepatitis C virus (HCV) remains a dangerous health problem for the reason that the mechanism of hepatocyte infection is still unknown. Hence, much attention has been put on the problem of interaction between HCV and human proteins. However, the research is still standing at the beginning point due to the lack of structure information of HCV and human proteins. We extracted the most representative...
We present a parallel computational environment used to determine conductivity properties of human head tissues when the effects of skull inhomogeneities are modeled. The environment employs a parallel simulated annealing algorithm to overcome poor convergence rates of the simplex method for larger numbers of head tissues required for accurate modeling of electromagnetic dynamics of brain function...
Mining useful information from a large amount of biological data is becoming important, but most data mining research in bioinformatics is limited to molecular sequence data. We have developed a set of algorithms for analyzing hydrogen bond and van der Waals interactions between protein and RNA. Analysis of the most representative set of protein-RNA complexes revealed several interesting observations:...
Spectral estimation has important applications to microarray time series analysis. For unevenly sampled data, a common spectral estimation technique is to use the Lomb-Scargle algorithm. In this paper, we introduce a new reconstruction algorithm and singular spectrum analysis (SSA) method to deal with unevenly sampled microarray time series. The new reconstruction method is based on signal reconstruction...
The Virtual Ecology Workbench (VEW) is a suite of utilities for creating, executing and analysing biological models of the ocean. At its core is a mathematical language allowing individual plankters to be modelled using equations from laboratory experiments. The language uses conventional mathematical assignments and seven plankton-specific functions. A model consists of a number of different plankton...
Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. These choices need not necessarily be mutually exclusive. We propose a hybrid agent-based approach where biological cells are modeled as individuals (agents) while chemical molecules are kept as quantities. This hybridization in entity representation entails...
This paper addresses the efficiency issues in solving large sparse linear systems parallely on scalar and vector architectures. Linear systems arise in numerous applications that need to solve PDEs on complex domains. The major time consuming part of large scale implicit Finite Element (FE) or Finite Volume (FV) simulation is solving the assembled global system of equations. First, the performance...
In this paper we conduct a detailed numerical analysis of the Gauss-type Nested Implicit Runge-Kutta formulas of order 4, introduced by Kulikov and Shindin in [4]. These methods possess many important practical properties such as high order, good stability, symmetry and so on. They are also conjugate to a symplectic method of order 6 at least. All of these make them efficient for solving many nonstiff...
In simulations of supernovae, linear systems of equations with a block penta-diagonal matrix possessing small, dense matrix blocks occur. For an efficient solution, a compact multiplication scheme based on a restructured version of the Thomas algorithm and specifically adapted routines for LU factorization as well as forward and backward substitution are presented. On a NEC SX-8 vector system, runtime...
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