Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike
Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike
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DOI：
10.1016/j.bpj.2023.01.042
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发表时间：
2023-07-25
影响因子：
3.4
通讯作者：
Bernardi，Rafael C.
中科院分区：
文献类型：
--
作者：
Melo，Marcelo C. R.;Bernardi，Rafael C.
世纪前，物理学家开始广泛依赖理论模型来指导新的实验。不久之后，化学家们开始做同样的事情。现在，生物学研究进入了一个实验与理论齐头并进的新时代。新的软件和专用硬件成为理解实验数据和提出新模型的必要条件。事实上，目前的千万亿次计算资源已经使研究人员能够达到前所未有的模拟吞吐量水平，以连接计算机和体外实验。成本的降低和访问的改善使大量研究小组能够采用超级计算资源和技术。在这里，我们概述了大规模计算如何发展，以扩大数十年的研究，激发新的研究工作，并不断连接模拟和观察。例如，多个公共和私人资助的团体投入了大量资源来开发用于计算生物物理学的人工智能工具，从加速量子化学计算到提出蛋白质结构模型。此外，计算机硬件的进步加速了单分子实验观察和整个细胞中发生的化学反应模拟的数据处理。软件和硬件的结合为艾级计算开辟了道路，并于2022年由橡树岭国家实验室揭幕的第一台公共艾级超级计算机Frontier的生产。最后，普及和发展计算技术以及培训研究人员使用这些技术只会加速后代工具和学习资源的多样化。
Over a century ago, physicists started broadly relying on theoretical models to guide new experiments. Soon thereafter, chemists began doing the same. Now, biological research enters a new era when experiment and theory walk hand in hand. Novel software and specialized hardware became essential to understand experimental data and propose new models. In fact, current petascale computing resources already allow researchers to reach unprecedented levels of simulation throughput to connect in silico and in vitro experiments. The reduction in cost and improved access allowed a large number of research groups to adopt supercomputing resources and techniques. Here, we outline how large-scale computing has evolved to expand decades-old research, spark new research efforts, and continuously connect simulation and observation. For instance, multiple publicly and privately funded groups have dedicated extensive resources to develop artificial intelligence tools for computational biophysics, from accelerating quantum chemistry calculations to proposing protein structure models. Moreover, advances in computer hardware have accelerated data processing from single-molecule experimental observations and simulations of chemical reactions occurring throughout entire cells. The combination of software and hardware has opened the way for exascale computing and the production of the first public exascale supercomputer, Frontier, inaugurated by the Oak Ridge National Laboratory in 2022. Ultimately, the popularization and development of computational techniques and the training of researchers to use them will only accelerate the diversification of tools and learning resources for future generations.