Nov, 3

Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Molecular dynamics (MD) simulation is a powerful computational tool to studythe behavior of macromolecular systems. But many simulations of this field arelimited in spatial or temporal scale by the available computational resource.In recent years, graphics processing unit (GPU) provides unprecedentedcomputational power for scientific applications. Many MD algorithms suit withthe multithread nature of GPU. In this […]
Nov, 2

On modelling of anisotropic viscoelasticity for soft tissue simulation: numerical solution and GPU execution

Efficient and accurate techniques for simulation of soft tissue deformation are an increasingly valuable tool in many areas of medical image computing, such as biomechanically-driven image registration and interactive surgical simulation. For reasons of efficiency most analyses are based on simplified linear formulations, and previously almost all have ignored well established features of tissue mechanical […]
Nov, 2

Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Units

PMID: 18229900 The modification of a general purpose code for quantum mechanical calculations of molecular properties (Q-Chem) to use a graphical processing unit (GPU) is reported. A 4.3x speedup of the resolution-of-the-identity second-order MollerPlesset perturbation theory (RI-MP2) execution time is observed in single point energy calculations of linear alkanes. The code modification is accomplished using […]
Nov, 2

CryptoGraphics: Secret Key Cryptography Using Graphics Cards

We study the feasibility of using Graphics Processing Units (GPUs) for cryptographic processing, by exploiting the ability for GPUs to simultaneously process large quantities of pixels, to offload symmetric key encryption from the main processor. We demonstrate the use of GPUs for applying the key stream when using stream ciphers. We also investigate the use […]
Nov, 2

GPU accelerated viscous-fluid deformable registration for radiotherapy

Repeated acquisitions of computed tomography and magnetic resonance imaging are increasingly used during radiotherapy treatment to accurately deliver radiation while limiting side effects. This is only feasible however after all acquisitions have been correlated to a single reference scan using a deformable registration method. This paper presents a parallel implementation of one such method, the […]
Nov, 2

Towards Utilizing GPUs in Information Visualization: A Model and Implementation of Image-Space Operations

Modern programmable GPUs represent a vast potential in terms of performance and visual flexibility for information visualization research, but surprisingly few applications even begin to utilize this potential. In this paper, we conjecture that this may be due to the mismatch between the high-level abstract data types commonly visualized in our field, and the low-level […]
Nov, 2

Discrete Wavelet Transform on Consumer-Level Graphics Hardware

Discrete wavelet transform (DWT) has been heavily studied and developed in various scientific and engineering fields. Its multiresolution and locality nature facilitates applications requiring progressiveness and capturing high-frequency details. However, when dealing with enormous data volume, its performance may drastically reduce. On the other hand, with the recent advances in consumer-level graphics hardware, personal computers […]
Nov, 2

Real-time optical manipulation of micron sized structures using GPU generated holograms

Holographic optical tweezers allow the three dimensional, dynamic, multipoint manipulation of micron sized dielectric objects. Exploiting the massive parallel architecture of modern GPUs we can generate highly optimized holograms at video frame rate allowing the interactive micro-manipulation of complex structures.
Nov, 2

Implementation of a Lattice–Boltzmann method for numerical fluid mechanics using the nVIDIA CUDA technology

The Lattice-Boltzmann method (LBM) is a distribution-function based approach to numerical fluid mechanics. Due to the simple formulation of the underlying algorithm this method is well suited for parallelization and hardware acceleration using general purpose graphical processing units (GPGPU). Within this work LBM has been implemented in a new code with multi-GPU support and physically […]
Nov, 2

Multilevel summation of electrostatic potentials using graphics processing units

Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applications requires the use of many-core processors and accelerators such as graphics processing units (GPUs). This paper discusses GPU acceleration of the multilevel summation method for […]
Nov, 2

Performance Predictions for General-Purpose Computation on GPUs

Using modern graphics processing units for no-graphics high performance computing is motivated by their enhanced programmability, attractive price/performance ratio and incredible growth in speed. Although the pipeline of a modern graphics processing unit (GPU) permits high throughput and more concurrency, they bring more complexities in analyzing the performance of GPU-based applications. In this paper, we […]
Nov, 2

Fast and accurate protein substructure searching with simulated annealing and GPUs

BACKGROUND: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) […]

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