Gotran provides a framework for working with systems of ordinary differential equations (ODEs): Its primary goal is to increase the workflow efficiency of computational modelling in biomedical research. The ODEs, given by the time derivative of state variables, are described in a Gotran form file and can be automatically translated into different outputs depending on […]

February 6, 2015 by hgpu

There is a significant reduction of processing time and speedup of performance in computer graphics with the emergence of Graphic Processing Units (GPUs). GPUs have been developed to surpass Central Processing Unit (CPU) in terms of performance and processing speed. This evolution has opened up a new area in computing and researches where highly parallel […]

July 18, 2014 by hgpu

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing […]

May 30, 2014 by hgpu

This paper deals with a Galerkin-based multi-scale time integration of a viscoelastic rope model. Using Hamilton’s dynamical formulation, Newton’s equation of motion as a second-order partial differential equation is transformed into two coupled first order partial differential equations in time. The considered finite viscoelastic deformations are described by means of a deformation-like internal variable determined […]

April 24, 2014 by hgpu

A recent development, called isogeometric analysis, provides a unified approach for design, analysis and optimization of functional products in industry. Common volume rendering methods for inspecting the results from the numerical simulations can not be applied directly to isogeometric models. We present a novel approach for interactive visualization of isogeometric analysis results, ensuring correct, i.e., […]

April 22, 2014 by hgpu

In this paper, we discuss parameter identification for models based on ordinary differential equations in the context of solid oxide fuel cells. In this case, verified methods (e.g. interval analysis), which provide a guarantee of correctness for the computed result, can be of great help for dealing with the appearing uncertainty and for devising accurate […]

October 15, 2013 by hgpu

Physical system models that consist of thousands of ordinary differential equations can be synthesized to field-programmable gate arrays (FPGAs) for highly-parallelized, real-time physical system emulation. Previous work introduced synthesis of custom networks of homogeneous processing elements, consisting of processing elements that are either all general differential equation solvers or are all custom solvers tailored to […]

August 23, 2013 by hgpu

The graphics processing unit (GPU) is recently used as a massively parallel processor to speed up general computation. However, the GPU can decrease the performance of irregular computation, because the GPU is based on the single instruction, multiple data (SIMD) architecture. The irregular computations here are conditional branches and memory accesses, which vary the behavior […]

June 18, 2013 by hgpu

The development of increasingly powerful and low cost massively parallel processors, known as GPUs, has created new opportunities for high speed and high precision computational work in physics. GPUs are extremely well suited to solving computationally intense problems at speeds much greater than traditional processors. They are now found in most personal computers, with research […]

May 19, 2013 by hgpu

Tornadoes such as Joplin, Mo (2011), Spencer, SD (1998), and Dallas, Texas (1957) induce extremely high wind velocities that devastate structures and lift off large objects in their path. Typically, a tornado takes up to an hour to materialize in the form of a narrow axisymmetric vortex and sustains that structure for 10-20 minutes after […]

April 25, 2013 by hgpu

The modeling of ion-transport through biological membranes is important for understanding many life processes. The transmembrane potential and ion concentrations in the stationary state can be measured in in-vivo experiments. They can also be simulated within membrane models. Here we consider a basic model of ion transport that describes the time evolution of ion concentrations […]

March 26, 2013 by hgpu

The presented contribution maps the possibilities of exploitation of the massive parallel computational hardware (namely GPU) for solution of the initial value problems of ordinary differential equations. Two cases are discussed: parallel solution of a single ODE and parallel execution of scalar ODE solvers. Whereas the advantages of the special architecture in the case of […]

February 27, 2013 by hgpu