Abstract-Molecular geometric properties, such as volume, exposed surface area, and occurrence of internal cavities, are important inputs to many applications in molecular modeling. In this work we describe a very general and highly efficient approach for the accurate computation of such properties, which is applicable to arbitrary molecular surface models. The technique relies on a high performance ray casting framework that can be easily adapted to the computation of further quantities of interest at interactive speed, even for huge models.
Figure 1: From left to right: Images of neghip (64 3 ), engine (256 2 × 110), foot (256 3 ), visible female slice (512 3 ), and foot close-up rendered with our optimized CUDA ray caster into 1024 2 window in 46.7, 30, 15.2, 11.6, and 11.8, respectively on a single GeForce 8800GT.
We present a novel software package for tomographic reconstruction in electron microscopy, named Ettention [1]. The software consists of a set of modular building-blocks for iterative reconstruction algorithms. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and user interface. We provide developers with a clean application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Several case studies are provided to demonstrate the feasibility of the concept [2].
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