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

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.