Title:	COMPUTING THE SOLVENT EXCLUDED VOLUME BY GPU-BASED RAY CASTING
Author(s):	Martin Manak
ISBN:	978-989-8533-79-1
Editors:	Katherine Blashki and Yingcai Xiao
Year:	2018
Edition:	Single
Keywords:	Volume, Ray Casting, GPU, Solvent Excluded Surface
Type:	Full Paper
First Page:	299
Last Page:	306
Language:	English
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Paper Abstract:	The solvent excluded surface (SES) is a hypothetical boundary between atoms of a molecule and a solvent. The volume of space bounded by this non-linear surface is a useful quantity in computational biochemistry. Among the approaches for the computation of the volume, there is one which estimates the volume by a numerical integration. Several rays passing through the surface are generated and the parts inside the surface are summed up. The previous approach was designed primarily for CPU and tested on triangular surfaces. In this paper, the previous approach is adapted to GPU. This computational environment offers a high level of parallelism. Previous shaders, designed primarily for rendering SES by ray casting on GPU, were modified to compute volume contributions along a ray. The problem with losing precision in the computation of intermediate results is solved by transforming floating-point numbers to big integers. Thread-safety is ensured by using atomic operations. There were also problems with long computations on some systems. They are solved by using several synchronization objects (fence-sync). Thanks to these improvements it was possible to greatly increase the resolution and speed of the original solution.
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