CRII: ACI: Algorithms and Tools to Facilitate the Development of High Fidelity Reactive Molecular Dynamics Models

CRII：ACI：促进高保真反应分子动力学模型开发的算法和工具

• 批准号: 1566049
• 负责人: Metin Aktulga
• 金额: $ 17.5万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-15 至 2019-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1566049&HistoricalAwards=false
• 关键词: CRII; ACI; Algorithms; Tools; Facilitate

Atomistic simulations enable understanding, analysis, and design of complex systems at spatio-temporal scales not easily accessible to experimental observation. Conventional molecular dynamics techniques have been applied with great success in application domains ranging from materials design to biophysical systems. Recent developments in reactive molecular dynamics have significantly extended the application scope of these techniques to systems that involve chemical bond activity. The core of these reactive atomistic simulations is a model for atomic interactions that describes the chemical structure of the domain, as well as its time evolution. This project aims to build a cyberinfrastructure to facilitate the development of highly resolved models of atomic interactions, along with their associated parameterizations. It will accomplish these goals through novel algorithms and software tools, reference datasets, and comprehensive validation in diverse application domains. The resulting infrastructure can enable computational scientists to develop high fidelity reactive force fields in a time and cost effective way. As a result, the accuracy and scope of reactive atomistic simulations have the potential to be increased significantly. The intellectual contributions of the project are complemented by education and outreach efforts that focus on interdisciplinary education through development and dissemination of instructional modules, publications, and presentations. Outreach efforts focus on recruitment of underrepresented minorities at the graduate level, and integration of undergraduate students into research efforts at an early stage. Therefore, this research aligns with the NSF mission to promote the progress of science and to advance the national health, prosperity and welfare.This project focuses on algorithms and software for the development and optimization of force fields for reactive molecular dynamics (MD) techniques. The fidelity of these simulations is critically dependent on the functional forms and parameterizations of the inter-atomic potentials. Traditionally, the development of inter-atomic potentials has involved significant domain expertise, and is highly time and labor-intensive. This project aims to design a powerful new cyberinfrastructure that integrates extraction of reference datasets, model selection and optimization algorithms, and comprehensive validation, to enable rapid prototyping and deployment of complex reactive atomistic models. In particular, reference datasets are selected for coverage as well as their impact on the inter-atomic potential, using novel procedures to minimize the requirements on quantum mechanical screenings. The process of optimizing the force field leverages this reference set and introduces a histogram based optimization technique for parameter sampling and selection. Finally, a novel API is proposed to enable the translation of suitable force fields from high-level mathematical descriptions into efficient parallel software. By automating each labor-intensive step along the way, the proposed framework aims to form a first-of-its-kind environment for development of high fidelity reactive MD models. Given the applicability of reactive MD models from materials modeling to biophysical simulations, the proposed cyberinfrastructure can help advance the state-of-the-art in advance materials design and drug discovery.

原子模拟使理解，分析和设计复杂的系统在时空尺度上不容易获得实验观察。传统的分子动力学技术已经成功地应用于从材料设计到生物物理系统的应用领域。反应分子动力学的最新发展，显着扩展了这些技术的应用范围，涉及化学键活性的系统。这些反应原子模拟的核心是原子相互作用的模型，它描述了域的化学结构及其时间演化。该项目旨在建立一个网络基础设施，以促进原子相互作用的高分辨率模型的开发，沿着其相关的参数化。它将通过新颖的算法和软件工具、参考数据集以及在不同应用领域的全面验证来实现这些目标。由此产生的基础设施可以使计算科学家以时间和成本效益的方式开发高保真反作用力场。因此，反应原子模拟的准确性和范围有可能显着增加。该项目的智力贡献得到了教育和外联工作的补充，这些工作通过开发和传播教学模块、出版物和演示文稿，侧重于跨学科教育。外展工作的重点是在研究生阶段招募代表性不足的少数族裔，并在早期阶段将本科生纳入研究工作。 因此，本研究符合美国国家科学基金会的使命，以促进科学的进步和促进国家的健康，繁荣和福利。本项目的重点是算法和软件的发展和优化力场的反应分子动力学（MD）技术。这些模拟的保真度是关键依赖于原子间势的函数形式和参数化。传统上，原子间相互作用势的发展涉及重要的领域专业知识，并且是高度时间和劳动密集型的。该项目旨在设计一个强大的新网络基础设施，集成参考数据集的提取，模型选择和优化算法以及全面的验证，以实现复杂反应原子模型的快速原型设计和部署。特别是，选择参考数据集来覆盖范围及其对原子间势的影响，使用新的程序来最大限度地减少对量子力学筛选的要求。优化力场的过程利用了该参考集，并引入了基于直方图的优化技术，用于参数采样和选择。最后，提出了一种新的API，使翻译合适的力场从高层次的数学描述到高效的并行软件。通过自动化每一个劳动密集型的步骤沿着的方式，所提出的框架的目的是形成一个第一的高保真反应MD模型的开发环境。鉴于反应性MD模型从材料建模到生物物理模拟的适用性，拟议的网络基础设施可以帮助推进先进材料设计和药物发现的最新技术。