Ion-molecule collision cross-section calculations using trajectory parallelization in distributed systems

Abstract

Ion Mobility coupled with Mass Spectrometry (IM-MS) stands as a strong analytical method for structurally characterizing complex molecules. In IM-MS, the sample under investigation is ionized and propelled by an electric field into a drift tube, which collides against a buffer gas. The separation of the ion gas phase is then measured through the differences in their rotationally averaged Collision Cross-Section (CCS) values. The effectiveness of the measured Collision Cross-Section (CCS) for structural characterization critically depends on the validation against theoretical calculations. This validation process relies on intensive molecular mechanics simulations, which can be computationally demanding, especially for large systems such as molecular assemblies and viruses. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS experimental data. This work presents the MassCCS software, which considerably increases the CCS simulation performance by implementing a linked-cell-based algorithm, incorporating High-Performance Computing (HPC) techniques. We performed extensive tests regarding the system size, shape, and number of CPU cores. Experimental results reveal speedups up to 3 orders of magnitude faster than Collision Simulator for Ion Mobility Spectrometry (CoSIMS) and High-Performance Collision Cross Section (HPCCS), optimized solutions for CCS simulations, for a single node execution. In addition, we extended MassCCS at the inter-node level by employing OpenMP Cluster (OMPC). OMPC is an innovative programming model designed for the development of HPC applications. It streamlines the development process and simplifies software maintenance using only OpenMP directives. Notably, OMPC delivers a performance level comparable to a pure MPI implementation. This enhancement enabled expensive CCS calculations using nitrogen buffer gas for large systems such as human adenovirus with ∼11 million atoms in just ∼4 min, making MassCCS the most performant software nowadays, to the best of our knowledge. MassCCS is available as free software for Academic use at https://github.com/cces-cepid/massccs.