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Abstract. Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) to design and implement a new parallel algorithm. This results in an implementation with significant runtime savings on an off-the-shelf computer graphics card.

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Nowadays, Computational Fluid Dynamics (CFD) methods play an important part in the production process of the automotive industry. Progress in recent years has made possible highly sophisticated airflow‐simulation models that are used in engineering for optimization and verification of aerodynamics. The key purpose of the Simulation Tool for Airflow in the human Nose (STAN), developed at the Darmstadt University of Technology in cooperation with the University Hospital in Greifswald, is to use these techniques to support the rhinosurgeon in diagnosis and planning of therapy (Frühauf T, Mlynski G. Simulation and visualization of the air flow in the human nose. Proceedings of the First World Congress on Computational Medicine, Austin, Texas, 1994). A system has been developed that realizes a three‐dimensional (3D) reconstruction of the endonasal cavities based on computer tomography (CT) scans. This semiautomatic reconstruction method requires minimal manual intervention. The surface model is used to create an unstructured 3D volume mesh suitable for finite volume simulations. In this way, an individual simulation based on patient‐specific data can be realized. At the University Hospital in Greifswald, experimental investigations and measurements are made in nasal models to verify the simulation result. The goal of this project is to investigate individual nasal complaints and to detect respiratory disorders. The surgeon should be able to simulate the disordered respiration before performing a surgical procedure, and thereby increase the effectiveness of surgical planning. Comp Aid Surg 5:175–179 (2000). © 2000 Wiley‐Liss, Inc.