CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Biophysics

Background:

• Collision cross section (CCS) calculations are vital for characterizing molecular properties.
• Existing methods like MOBCAL can be computationally intensive, limiting throughput.
• Efficient simulation of buffer gas-ion collisions is crucial for accurate CCS determination.

Purpose of the Study:

• Introduce CoSIMS, a novel multithreaded software platform for trajectory-based CCS calculations.
• Compare CoSIMS performance against the established MOBCAL software.
• Evaluate the efficiency and accuracy of CoSIMS for diverse molecular systems.

Main Methods:

• CoSIMS utilizes molecular mechanics algorithms to reduce computational load.
• Key optimizations include neglecting long-range London dispersion interactions.
• An ellipsoidal projection approximation removes insignificant trajectories, enhancing speed.

Main Results:

• CoSIMS calculates CCS for fullerenes, proteins, and DNA strands.
• For elongated molecules like DNA, CoSIMS provides faster and more reasonable CCS than MOBCAL.
• CoSIMS reproduces MOBCAL's CCS for other molecules within a few percent accuracy.
• CoSIMS achieves near-identical CCS results as MOBCAL with approximately 100 times less CPU time.

Conclusions:

• CoSIMS offers a significant speedup for CCS calculations compared to MOBCAL.
• The implemented numerical methods make CoSIMS computationally efficient, even on a single core.
• CoSIMS is a viable and accelerated alternative for CCS calculations across various molecular types.