SI2-SSE: Enabling Chemical Accuracy in Computer Simulations: An Integrated Software Platform for Many-Body Molecular Dynamics

SI2-SSE：实现计算机模拟中的化学准确性：多体分子动力学集成软件平台

基本信息

批准号：
1642336
负责人：
Francesco Paesani
金额：
$ 49.99万
依托单位：
University of California-San Diego
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：
2017-04-01 至 2020-03-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1642336&HistoricalAwards=false
关键词：
SI2 SSE Enabling Chemical Accuracy

项目摘要

This project is jointly funded by the Office of Advanced Cyberinfrastructure and and the Division of Chemistry within the Directorate of Mathematical and Physical Sciences. As attested by the 2013 Nobel Prize in Chemistry awarded to Martin Karplus, Michael Levitt, and Arieh Warshel, molecular-level computer simulations have become indispensable in many research areas, including chemistry, physics, materials science, and biochemistry, and often provide fundamental insights that are otherwise difficult to obtain. Nowadays, computer simulations are used to complement, guide, and sometimes replace experimental measurements, reducing the amount of time and money spent on research to bring ideas from the lab to practical applications. In the pharmaceutical industry computer simulations play a key role in structure-based drug design as demonstrated by the development of HIV protease inhibitors. In the chemical industry, computer modeling guides the design of new catalysts as well as novel materials for applications in more efficient batteries, and fuel and solar cells. More recently, there has been significant success in using of computer simulations to design more effective chemical processes as well as to provide information on safety issues. However, both the realism and the predictive power of a molecular-level computer simulation directly depend on the accuracy with which the interactions between molecules are described. To address the limitations of existing simulation approaches, the project group has recently developed a new theoretical/computational methodology that has been shown to display unprecedented accuracy when applied to a variety of molecular systems. The overarching goal of the proposed research is the implementation of this new methodology into an integrated and publicly available software platform that will allow the scientific community to address a broad range of problems through computer simulations. Potential applications include, but are not limited to, the rational design of new drugs as well as novel materials for water purification and the detection of toxic compounds and explosives, the virtual screening of catalysts for more efficient chemical processes, the development of new batteries, solar and fuel cells, and biomolecular structure prediction. A diverse group of high school, undergraduate, and graduate students will be directly involved in different aspects of the proposed research. The students will thus acquire critical knowledge about computer simulations and programming, which will significantly enhance their competitiveness in today's computer-driven job market. Given its multidisciplinary and multifaceted nature, the proposed research will promote scientific progress at different levels and contribute to the development of new technologies that will advance the national health, prosperity and welfare, as well as secure the national defense.The proposed research focuses on the development and implementation of unique software elements that will enable computer simulations on both CPU and GPU architectures using the so-called many-body molecular dynamics (MB-MD) methodology developed by the Paesani group. These software elements will be made publicly available to the scientific community through an integrated platform. MB-MD is a new simulation methodology that has already been shown to provide unprecedented accuracy in molecular simulations of a variety of molecular systems from the gas to the condensed phase. The new software elements comprise three components integrated in a unique software platform: a suite of publicly available computational tools for the automated generation of many-body potential energy functions from electronic structure data; a client-server architecture for the calculation of the required electronic structure data through volunteer computing; independent CPU and GPU plugins for the OpenMM toolkit which will enable MB-MD simulations of generic molecular systems across different phases. In parallel with the proposed research and software engineering projects, outreach and mentoring activities to promote STEM disciplines among students from underprivileged and underrepresented minorities through the PI and Co-PI direct involvement in several outreach programs at UC San Diego and the San Diego Supercomputer Center. These activities are specifically designed to increase the involvement and advancement of women, minorities, and economically disadvantaged groups across different education levels, from high school to undergraduate and graduate students.

该项目由高级网络基础设施办公室以及数学和物理科学局内的化学划分共同资助。正如2013年诺贝尔化学奖所证明的那样，在许多研究领域，分子级的计算机模拟在许多研究领域都必不可少，包括化学，物理学，材料科学和生物化学，并且经常提供难以获得的基本见解，这是必不可少的。如今，计算机模拟被用来补充，指导，有时会取代实验测量，从而减少了在研究上花费的时间和金钱，以将实验室的想法带到实际应用。在制药行业中，计算机模拟在基于结构的药物设计中起着关键作用，如HIV蛋白酶抑制剂的发展所证明。在化学工业中，计算机建模指导新催化剂的设计以及用于更有效的电池以及燃料和太阳能电池的新颖材料。最近，在使用计算机模拟设计更有效的化学过程以及提供有关安全问题的信息方面取得了重大成功。但是，分子级计算机模拟的现实主义和预测能力直接取决于描述分子之间相互作用的准确性。为了解决现有模拟方法的局限性，该项目组最近开发了一种新的理论/计算方法，当应用于各种分子系统时，已显示出显示前所未有的准确性。拟议研究的总体目标是将这种新方法实施到一个集成且可公开的软件平台中，该平台将使科学界能够通过计算机模拟解决广泛的问题。潜在的应用包括但不限于新药的合理设计以及用于水净化的新型材料以及检测有毒化合物和爆炸物的材料，催化剂的虚拟筛选以进行更有效的化学过程，开发新的电池，太阳能和燃料电池，以及生物分子结构的预测。一群高中，本科和研究生将直接参与拟议研究的不同方面。因此，学生将获得有关计算机模拟和编程的重要知识，这将大大提高他们在当今计算机驱动的就业市场中的竞争力。 Given its multidisciplinary and multifaceted nature, the proposed research will promote scientific progress at different levels and contribute to the development of new technologies that will advance the national health, prosperity and welfare, as well as secure the national defense.The proposed research focuses on the development and implementation of unique software elements that will enable computer simulations on both CPU and GPU architectures using the so-called many-body molecular dynamics (MB-MD) methodology由Paesani集团开发。这些软件元素将通过集成平台公开向科学界公开使用。 MB-MD是一种新的模拟方法，已经证明可以在从气体到凝结相的各种分子系统的分子模拟中提供前所未有的精度。新的软件元素包括在独特的软件平台中集成的三个组件：一套公共可用的计算工具，用于从电子结构数据中自动生成多体势能函数；通过志愿者计算计算所需的电子结构数据的客户端服务器架构；用于OpenMM工具包的独立CPU和GPU插件，将在不同阶段启用通用分子系统的MB-MD模拟。与拟议的研究和软件工程项目同时，通过PI和Co-Pi直接参与UC Saniego和San Diego Supercuter Center的多个推出计划，从而促进来自弱势群体和代表性少数群体的学生的STEM学科。这些活动是专门设计的，以增加不同教育水平的妇女，少数民族和经济弱势群体的参与和进步，从高中到本科生和研究生。