Related papers: GPU-powered Simulation Methodologies for Biologica…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
Despite the recent advances in graphics hardware capabilities, a brute force approach is incapable of interactively displaying terabytes of data. We have implemented a system that uses hierarchical level-of-detailing for the results of…
Study of general purpose computation by GPU (Graphics Processing Unit) can improve the image processing capability of micro-computer system. This paper studies the parallelism of the different stages of decimation in time radix 2 FFT…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
Simulating the flow of different fluids can be a highly computational intensive process, which requires large amounts of resources. Recently there has been a lot of research effort directed towards GPU processing, which can greatly increase…
Simulation models are widely used in practice to facilitate decision-making in a complex, dynamic and stochastic environment. But they are computationally expensive to execute and optimize, due to lack of analytical tractability. Simulation…
With the development of artificial intelligence techniques, transportation system optimization is evolving from traditional methods relying on expert experience to simulation and learning-based decision and optimization methods.…
Modeling data sharing in GPU programs is a challenging task because of the massive parallelism and complex data sharing patterns provided by GPU architectures. Better GPU caching efficiency can be achieved through careful task scheduling…
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
This dissertation presents the design, implementation and evaluation of GPU-accelerated simulation frameworks for Evolutionary Spatial Cyclic Games (ESCGs), a class of agent-based models used to study ecological and evolutionary dynamics.…
Beagle is a new software framework that enables execution of Genetic Programming tasks on the GPU. Currently available for symbolic regression, it processes individuals of the population and fitness cases for training in a way that…
Ray tracing is a technique for generating an image by tracing the path of light through pixels in an image plane and simulating the effects of high-quality global illumination at a heavy computational cost. Because of the high computation…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
Simulation offers a simple and flexible way to estimate the power of a clinical trial when analytic formulae are not available. The computational burden of using simulation has, however, restricted its application to only the simplest of…
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…
Computing on graphics processors is maybe one of the most important developments in computational science to happen in decades. Not since the arrival of the Beowulf cluster, which combined open source software with commodity hardware to…