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.
The main goal of the project is to provide a scalable state of the art computational software platform for (quasi-) electrostatic ion optics calculations and motion dynamics simulations for multiple (>10^5) interacting ions as a service and as a standalone application for the researches and engineers working in the field of mass spectrometry instrumentation development. During Phase I of the project, we have used parallel processing algorithms to implement several main components of the platform. The code we have created uses parallel processing capabilities of the multicore processors and graphics processing units of desktop computers for calculations of the electric fields and charged particles motion simulations. The field of mass spectrometry has revolutionized many research and application areas. Mass spectrometry based methods play key roles in biomedical research enabling detection and identification of small molecule metabolites, lipids, and proteins embedded in such complex matrices as tissues and biological fluids. Nowadays, mass spectrometry has a central role in public safety, industrial hygiene, food safety, and many other application areas. Mass spectrometry based methods have traditionally been a benchmark in fundamental physics research, and will continue to be so in the foreseeable future. It is of the utmost importance to provide researchers and engineers with the appropriate tools that would enable them to predict the effects of the mass analyzer and ion optics parameters on the instrumental performance before building an instrument. For example, space-charge effects due to the presence of abundant ions are currently major factors to limiting the mass accuracy and dynamic range in mass spectrometry. Unfortunately, there are no widely available, affordable software tools to assess this problem. The computational software platform we are developing will provide the research and engineering mass spectrometry instrumentation communities with the state of the art tools that will allow performing intricate simulations on desktop computers in a reasonable timeframe.
