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

这个小型企业创新研究计划(SBIR)第一阶段项目专注于开发一个可扩展的高性能计算软件平台，用于模拟准静态离子光学器件和这些器件中许多(超过100万)带电粒子的运动动力学。虽然许多离子的存在引起的空间电荷效应是限制现代质谱学质量精度和动态范围的主要因素，但目前还没有广泛可用的软件工具来评估这一问题。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。该平台将结合一系列先进的功能，包括：实现最先进的并行处理计算方法，如并行拉普拉斯方程求解器、基于并行质点法的并行泊松方程求解器和利用并行3D快速傅立叶变换方法，利用格林函数方法考虑离子-电极相互作用；支持异构型高性能计算机硬件(从配备图形处理单元的台式计算机到异构型计算机集群、云计算平台和超级计算机)。这个项目的更广泛的影响/商业潜力可以通过使用关键计算算法和工具来实现，这些关键计算算法和工具将被开发用于计算生物学、蛋白质动力学的分子模拟、分子医学、用于药物发现的分子动力学(MD)模拟、蛋白质折叠的3D分子动力学(尤其是在利用基于质谱学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集群分析的MD、用于使用图形处理单元的台式计算机上的蛋白质模拟的超级计算机级采样、用于台式计算机上的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，充电等离子体系统、生物传感器等)。拟议的项目能够显著提高质谱学仪器领域的研究人员和工程师的生产率，并通过这一进步，加快从基础物理到生物技术和医学等其他研究和应用领域的发展步伐，在这些领域，质谱学发挥着关键的促进作用。

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.