Neighbor search algorithm for lattice-free simulations with short-range forces

We have recently developed a lattice-free simulation program in computational cell biology which needs the introduction and management of the biomechanical interactions of cells. These interactions are associated with short range forces which act on nearest-neighbors only. The forces act in the rear...

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Published in2014 International Conference on High Performance Computing & Simulation (HPCS) pp. 621 - 626
Main Authors Stella, S., Dogo, F., Milotti, E., Chignola, R.
Format Conference Proceeding
LanguageEnglish
Published IEEE 01.07.2014
Subjects
Biological system modeling
Computational modeling
Computer architecture
Graphics processing units
Mathematical model
Microprocessors
Tumors
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Summary:We have recently developed a lattice-free simulation program in computational cell biology which needs the introduction and management of the biomechanical interactions of cells. These interactions are associated with short range forces which act on nearest-neighbors only. The forces act in the rearrangement of cells due to proliferation and cell growth and this requires a recalculation of the proximity relations at each time step. Here we describe the implementation of an algorithm to efficiently compute the proximity relations and designed to run on Graphics Processing Units (GPUs). The results of the first test runs on an NVidia Fermi GPU are encouraging: the algorithm has the potential to significantly boost the simulation program and to map the disordered lattice also on other multicore machines with hypercubic connectivity.
ISBN:9781479953127
1479953121
DOI:10.1109/HPCSim.2014.6903745