Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …

The development of detailed, coherent, models of complex biological systems is recognized
as a key requirement for integrating the increasing amount of experimental data. In addition …

Graphics processing units (GPUs) have traditionally been used in molecular modeling solely
for visualization of molecular structures and animation of trajectories resulting from …

In the last years, graphics processing units (GPUs) witnessed ever growing applications for
a wide range of computational analyses in the field of life sciences. Despite its large …

Motivation: Mathematical modelling is central to systems and synthetic biology. Using
simulations to calculate statistics or to explore parameter space is a common means for …

We test the relative performances of two different approaches to the computation of forces for
molecular dynamics simulations on graphics processing units. A “vertex‐based” approach …

GPUs offer drastically different performance characteristics compared to traditional multicore
architectures. To explore the tradeoffs exposed by this difference, we refactor MUMmer, a …

The graphics processing unit (GPU), which originally was used exclusively for visualization
purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through …

Today's graphics processing units (GPUs) compose the scene from individual triangles. As
about 320 triangles are needed to approximate a single sphere—an atom—in a convincing …

Recent advances in experimental structure determination provide a wealth of structural data
on huge macromolecular assemblies such as the ribosome or viral capsids, available in …