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Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations

机译:图形处理单元上的Smoldyn:大规模并行布朗动力学模拟

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Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output.
机译:空间是生化系统模拟中非常重要的方面。最近,对能够应对空间的仿真算法的需求变得越来越迫切。生化系统的复杂而详细的模型需要处理单个分子和颗粒的运动,同时要考虑局部波动,运输现象和扩散。空间模型的一个常见缺点在于它们的复杂性:模型可能变得非常大,并且它们的仿真可能很耗时,尤其是如果我们想使用随机方法结合高空间分辨率以可靠的方式捕获系统行为时。为了兑现系统生物学的诺言,以便能够理解整个系统,我们需要从顺序仿真算法到并行仿真算法,扩大能够仿真的模型的规模。在本文中,我们分析了Smoldyn,这是一种具有空间分辨率和单分子详细信息的化学反应随机模拟的广泛分散算法,并且我们提出了利用图形处理单元(GPU)并行性的替代性创新实现。该实现在GPU上执行最复杂的计算步骤(扩散,单分子和双分子反应的计算,以及最常见的分子与表面相互作用的情况),并在系统的每个分子上并行计算它们。该实现提供了良好的加速比和实时,高质量的图形输出。

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