MRI: Acquisition of a GPU-Enabled Computer Cluster for Molecular Modeling Applications

MRI：获取支持 GPU 的计算机集群用于分子建模应用

• 批准号: 1726332
• 负责人: Christine Aikens
• 金额: $ 35万
• 依托单位: Kansas State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2020-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1726332&HistoricalAwards=false
• 关键词: MRI; Acquisition; GPU; Enabled; Computer

This award is supported by the Major Research Instrumentation (MRI), the Chemistry Research Instrumentation, and the Experimental Program to Stimulate Competitive Research (EPSCoR) programs. Professor Christine Aikens from Kansas State University and colleagues Paul Smith, Daniel Andresen, Bin Liu, and Jeffrey Comer are acquiring a graphic processing unit (GPU) computer cluster. In general, computer clusters are constructed with central processing units (CPU) as the core computational hardware. GPUs were subsequently developed as processing units and used to accelerate the video display on computer monitors. Computational scientists have found a combination of CPU/GPU systems are especially fast for certain computations, especially simulations. Software developed for computational simulations have reached the stage at which they can provide quantitative or semi-quantitative accuracy for a variety of molecular, biomolecular, nanoparticle, and materials modeling applications. These simulations provide needed atomic-level insight into chemical mechanisms and biological interactions that are difficult to study experimentally. This system provides for the computational needs of molecular modeling applications across chemistry, physics, engineering and biology. This system is used for research and training at Kansas State University. Researchers from across the state including those at community colleges, non-Ph.D. granting institutions, and minority-serving institutions also have access to this system and receive significant computing time.This computer cluster enhances research and education. It aids the modeling nanomaterials; understanding the fundamentals of electron-electron and electron-nuclear interactions. This cluster is also used in elucidating the factors involved in determining the selectivities of alcohol dehydration products on zeolite catalysts and carrying out protein-nanoparticle modeling to understand protein conformational transitions that sample relevant protein-surface configurations. The computer cluster is used in understanding denatured state ensembles in protein folding and understanding the role of protein aggregation which may be relevant to Alzheimer's disease.

该奖项由主要研究仪器(MRI)、化学研究仪器和刺激竞争性研究的实验计划(EPSCoR)项目支持。堪萨斯州立大学的克里斯汀·艾肯斯教授和他的同事保罗·史密斯、丹尼尔·安德森、刘斌和杰弗里·科默正在收购一个图形处理单元(GPU)计算机集群。一般而言，计算机集群是以中央处理器(CPU)作为核心计算硬件来构建的。图形处理器随后被开发为处理单元，并用于加速计算机显示器上的视频显示。计算科学家发现，CPU/GPU系统的组合对于某些计算特别快，特别是模拟。为计算模拟开发的软件已经达到了能够为各种分子、生物分子、纳米颗粒和材料建模应用提供定量或半定量精度的阶段。这些模拟提供了对难以通过实验研究的化学机制和生物相互作用所需的原子水平的洞察。该系统可满足化学、物理、工程和生物学等领域的分子建模应用的计算需求。该系统用于堪萨斯州立大学的研究和培训。来自全州各地的研究人员，包括社区大学、非博士授予机构和少数族裔服务机构的研究人员也可以访问这个系统，并获得大量的计算时间。这个计算机集群促进了研究和教育。它有助于模拟纳米材料；理解电子-电子和电子-核相互作用的基本原理。该簇还用于阐明决定沸石催化剂上乙醇脱水产物的选择性的因素，并进行蛋白质-纳米颗粒建模以了解蛋白质构象转变，从而采样相关的蛋白质-表面构型。计算机集群被用来理解蛋白质折叠中的变性状态集合，以及理解蛋白质聚集的作用，这可能与阿尔茨海默病有关。

项目成果

Electronic relaxation dynamics in [Au 25 (SR) 18 ] −1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) thiolate-protected nanoclusters

[Au 25 (SR) 18 ] â1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) 硫醇盐保护的纳米团簇中的电子弛豫动力学

• DOI: 10.1039/c9cp04039k
• 发表时间: 2020
• 期刊: Physical Chemistry Chemical Physics
• 影响因子: 3.3
• 作者: Senanayake, Ravithree D.;Aikens, Christine M.
• 通讯作者: Aikens, Christine M.

Comparison and convergence of optical absorption spectra of noble metal nanoparticles computed using linear-response and real-time time-dependent density functional theories

• DOI: 10.1016/j.comptc.2018.11.005
• 发表时间: 2018-12
• 期刊: Computational and Theoretical Chemistry
• 影响因子: 2.8
• 作者: K. Weerawardene;Christine M. Aikens

Modeling C–H Bond Activation and Oxidations of Alkanes over Cu–MOR Using First-Principles Methods

使用第一性原理方法对 Cu-MOR 上的 C-H 键活化和烷烃氧化进行建模

• DOI: 10.1021/acs.jpcc.9b00194
• 发表时间: 2019
• 期刊: The Journal of Physical Chemistry C
• 作者: Xu, Jiayi;Liu, Bin
• 通讯作者: Liu, Bin

Enhancing Methanol Oxidation Reaction with Platinum‐based Catalysts using a N‐Doped Three‐dimensional Graphitic Carbon Support

• DOI: 10.1002/cctc.202001162
• 发表时间: 2020-12
• 期刊: ChemCatChem
• 影响因子: 4.5
• 作者: Ayyappan Elangovan;Jiayi Xu;Archana Sekar;B. Liu;Jun Li

Theoretical Analysis of Optical Absorption Spectra of Parallel Nanowire Dimers and Dolmen Trimers

平行纳米线二聚体和支石三聚体光学吸收光谱的理论分析

• DOI: 10.1021/acs.jpcc.0c04419
• 发表时间: 2020
• 期刊: The Journal of Physical Chemistry C
• 作者: Pandeya, Pratima;Aikens, Christine M.
• 通讯作者: Aikens, Christine M.