New Numerical Solutions for Density Functional Theory

密度泛函理论的新数值解

• 批准号: 7159465
• 负责人: JING KONG
• 金额: $ 32.75万
• 依托单位: Q-CHEM, INC.
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-03-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7159465
• 关键词: bacteriorhodopsins; bioenergetics; biophysics; computer simulation; data collection methodology /evaluation; density; mathematical model; model design /development; molecular dynamics; quantum chemistry; statistics /biometry

DESCRIPTION (provided by applicant): First principle (ab initio) quantum chemistry methods are widely used for computational studies in biology, chemistry and material science. Among the various quantum chemistry models, density functional theory (DFT) offers a good balance between computational cost and accuracy and accordingly is the most widely used method in many scientific fields, including biological research. However, despite the remarkable advances in DFT in the past decade, the application of DFT to treat large biological systems or molecular dynamics is still limited by computational cost. Accordingly, the goal of the research proposed here is to increase the efficiency of DFT calculations by several fold through the implementation of novel algorithms. There are two major time-consuming parts in a DFT calculation, namely computation of the Coulomb and the exchange-correlation (XC) contributions. In the Phase I of this project, we implemented the Fourier Transform Coulomb method for the evaluation of the Coulomb contribution, and developed a new algorithm called multiresolution XC (mrXC), for the evaluation of XC contribution to the DFT energy with local functionals. The results show that FTC accelerates Coulomb calculation by up to a factor of 4.5 over the most efficient Coulomb algorithms. The mrXC method speeds up the calculation of XC contribution by as much as a factor of 5. In the Phase II of the project, we will develop and implement FTC and mrXC for the most widely used components of DFT calculations, including energy and gradients with respect to nuclear motions for both ground and excited states. Efforts will also be made to further improve the efficiency. Formulism will also be developed at the level of general-gradient approximation, the mostly widely used type of DFT functional. In order to demonstrate the utility of DFT algorithms developed here, we will carry out a state-of-the-art computational study of the mechanism of light-induced structural change in bacteriorhodopsin. These improvements will significantly increase Q-Chem users? productivity and greatly extend the complexity of molecular systems that can be studied using DFT. Furthermore, it will bring DFT much closer to our goal of being able to replace the less accurate but computationally less demanding models currently used today in molecular dynamics or Monte Carlo simulations of proteins and other large molecular systems. This project aims to improve the efficiency of the density-functional theory (DFT) calculations. DFT is at the core of molecular modeling and is applied widely in biological research/development and in drug discovery. The improved DFT will significantly increase researchers' productivity and extend its application scope.

描述（由申请人提供）：第一原理（从头算）量子化学方法广泛用于生物学、化学和材料科学中的计算研究。在各种量子化学模型中，密度泛函理论（DFT）在计算成本和准确性之间提供了良好的平衡，因此在许多科学领域（包括生物研究）中使用最广泛的方法。然而，尽管DFT在过去的十年中取得了显着的进展，DFT的应用处理大型生物系统或分子动力学仍然受到计算成本的限制。因此，这里提出的研究的目标是通过实施新的算法，提高DFT计算的效率几倍。在DFT计算中有两个主要的耗时部分，即库仑和交换相关（XC）贡献的计算。在这个项目的第一阶段，我们实现了傅里叶变换库仑方法的库仑贡献的评估，并开发了一种新的算法称为多分辨率XC（mrXC），用于评估XC的DFT能量与本地泛函的贡献。结果表明，FTC加速库仑计算高达4.5倍以上的最有效的库仑算法。mrXC方法将XC贡献的计算速度提高了5倍。在该项目的第二阶段，我们将开发和实施FTC和mrXC，用于DFT计算中最广泛使用的组件，包括基态和激发态核运动的能量和梯度。还将努力进一步提高效率。公式也将在一般梯度近似的水平上开发，这是DFT泛函的最广泛使用的类型。为了证明DFT算法的实用性，我们将进行一个国家的最先进的计算研究的光诱导细菌视紫红质的结构变化的机制。这些改进将大大增加Q-Chem用户？生产力和大大扩展的复杂性，可以使用DFT研究的分子系统。此外，它将使DFT更接近我们的目标，即能够取代目前在分子动力学或蛋白质和其他大型分子系统的蒙特卡罗模拟中使用的不太准确但计算要求不高的模型。该项目旨在提高密度泛函理论（DFT）计算的效率。密度泛函理论是分子建模的核心，广泛应用于生物研究/开发和药物发现。改进后的DFT将显著提高研究人员的工作效率，扩大其应用范围。