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首页> 外文会议>International Convention on Information and Communication Technology, Electronics and Microelectronics >Exploring bacterial biofilms with NAMD, a highly scalable parallel code for complex molecular simulations
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Exploring bacterial biofilms with NAMD, a highly scalable parallel code for complex molecular simulations

机译：使用NAMD探索细菌生物膜，NAMD是用于复杂分子模拟的高度可扩展并行代码

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Bacterial biofilms are highly complex structures. We are more and more recognizing that bacterial biofilms are predominant forms of the bacterial existence against the planktonic one. Under certain circumstances, bacteria starts to build biofilm and forms 3D structure, so called extracellular matrix. Hulled within this matrix, bacteria becomes more prone to host defense mechanisms and most antibiotics, thus expressing considerably higher virulence and antibiotic resistance than its planktonic form. Because of their importance, numerous researchers investigated bacterial biofilms in the last decades, using numerous methods, like electron microscopy, mass spectroscopy and nuclear magnetic resonance. However, neither of these methods is able to reveal an exact structure of extracellular matrix. Exploring dynamics of extracellular matrix is even more complex, and out of the reach for known analysis methods. For these reasons, there is a need for more effective method, and this could be computer driven simulation. In order to check if it could be a method of choice, we estimated the computational resources needed to simulate the bacterial biofilm. We found that possibility of performing this simulation in the reasonable time on fastest supercomputers today does not exists, and will not be available until at least 2028. For this reason, we explored possibilities of running NAMD based bacterial biofilms simulations on Cloud, and landed with the same conclusion. Besides, we found that for both approaches NAMD has to extend its scalability from about current 500.000 cores to many millions of cores in the future.
机译：细菌生物膜是高度复杂的结构。我们越来越认识到细菌生物膜是对抗浮游生物的主要细菌存在形式。在某些情况下，细菌开始建立生物膜并形成3D结构，即所谓的细胞外基质。细菌被包裹在这种基质中，变得更易于宿主防御机制和大多数抗生素，因此比浮游生物具有更高的毒力和抗生素抗性。由于它们的重要性，在过去的几十年中，许多研究人员使用了许多方法，例如电子显微镜，质谱和核磁共振，对细菌生物膜进行了研究。然而，这些方法均不能揭示细胞外基质的确切结构。探索细胞外基质的动力学更加复杂，这对于已知的分析方法是遥不可及的。由于这些原因，需要一种更有效的方法，这可以是计算机驱动的仿真。为了检查它是否可以作为一种选择方法，我们估算了模拟细菌生物膜所需的计算资源。我们发现在当今最快的超级计算机上在合理的时间内执行此模拟的可能性并不存在，并且至少要到2028年才可用。因此，我们探索了在Cloud上运行基于NAMD的细菌生物膜模拟的可能性，并在同样的结论。此外，我们发现，对于这两种方法，NAMD都必须将其可扩展性从目前的约50万个内核扩展到未来的数百万个内核。

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