SBIR Phase I: Making new standard in simulation of ion optical problems

SBIR 第一阶段：制定离子光学问题模拟的新标准

• 批准号: 1315302
• 负责人: Alexander Misharin
• 金额: $ 14.68万
• 依托单位: Masstech
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-01 至 2014-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1315302&HistoricalAwards=false
• 关键词: SBIR; Phase; Making; new; standard

This Small Business Innovation Research Program (SBIR) Phase I project is focused on the development of a scalable high performance state of the art computational software platform for simulation of the quasi-static ion optics devices and motion dynamics of many (more than 1 million) charged particles in those devices. While space charge effects due to presence of many ions is currently a major factor limiting the mass accuracy and dynamic range in modern mass spectrometry, there are no widely available software tools to assess this problem. The proposed platform will provide tools for researches in academia and industry to address this and many other problems. The platform will combine a number of advanced features including: implementation of the state of the art parallel processing computational methods such as a parallel Laplace's equation solver, a parallel Poisson equation solver based on a parallel particle-in-cell method and utilization of the parallel 3D fast Fourier transformation method, utilization of the Green's Function method to take ion-electrode interactions into account; support of the heterogeneous high performance computer hardware (starting from a desktop computer equipped with graphics processing unit to heterogeneous computer clusters, cloud computing platforms, and supercomputers). The broader impact/commercial potential of this project can be achieved by use of the key computational algorithms and tools that will be developed for parallel particle-in-cell -based Poisson equation solver and parallel ion motion simulations in the areas of computational biology, molecular simulations of protein dynamics, molecular medicine, molecular dynamics (MD) simulations for drug discovery, 3D molecular dynamics of protein folding (especially when augmented with the information provided by the mass spectrometry-based methods of protein analysis), MD for clusters analysis of bio-molecular systems, supercomputer-level sampling for protein simulation on desktop computers using graphics processing units, computational nanotechnology (e.g. molecular electronics, charged plasma systems, bio-sensors, etc.). The proposed project is capable of significantly increasing the productivity of the researchers and engineers in the mass spectrometry instrumentation field and, by the virtue of this advancement, to increase the pace of the developments in the other research and application areas, ranging from fundamental physics to biotechnology and medicine, for which mass spectrometry plays key enabling roles.

这个小企业创新研究计划（SBIR）第一阶段项目的重点是开发一个可扩展的高性能最先进的计算软件平台，用于模拟准静态离子光学设备和这些设备中许多（超过100万）带电粒子的运动动力学。虽然由于许多离子的存在而导致的空间电荷效应目前是限制现代质谱法中的质量准确度和动态范围的主要因素，但是没有广泛可用的软件工具来评估该问题。拟议的平台将为学术界和工业界的研究提供工具，以解决这一问题和许多其他问题。该平台将结合联合收割机许多先进的特征，包括：实现最先进的并行处理计算方法，例如并行拉普拉斯方程求解器、基于并行粒子单元法的并行泊松方程求解器和利用并行3D快速傅立叶变换法、利用绿色函数法来考虑离子-电极相互作用;支持异构高性能计算机硬件（从配备图形处理单元的台式计算机到异构计算机集群、云计算平台和超级计算机）。该项目的更广泛的影响/商业潜力可以通过使用关键的计算算法和工具来实现，这些算法和工具将在计算生物学、蛋白质动力学的分子模拟、分子医学、药物发现的分子动力学（MD）模拟、蛋白质折叠的三维分子动力学（特别是当用基于质谱的蛋白质分析方法提供的信息增强时），用于生物分子系统的聚类分析的MD，使用图形处理单元在台式计算机上进行蛋白质模拟的超级计算机级采样，计算纳米技术（例如分子电子学、带电等离子体系统、生物传感器等）。拟议的项目能够显著提高质谱仪器领域研究人员和工程师的生产力，并凭借这一进步，加快其他研究和应用领域的发展步伐，从基础物理到生物技术和医学，质谱起着关键的促进作用。