Numerical simulation of the evolution of ion clouds in a mass spectrometer by the particle-in-cell method

At present, mass spectrometry is the main analytical technique used in the studies on determining the composition of biomolecules. In such studies, the accuracy of determining the mass values is affected by hidden parameters (Coulomb interaction of analyzed ions with each other and with the walls of the mass-spectrometer trap).The problem consists in the development of a parallel computer code that allows simulation of the millions of charged ions and can reproduce the times of a real experiment in order to study the influence of Coulomb forces on the mass spectrum.The mathematical formulation of the original physical problem is presented. It is proposed to use the particle-in-cell method for simulation of the motion of ion clouds in the trap. The equations of motion are integrated with the use of a scheme with frequency correction. This approach ensures exact reproduction of the cyclotron motion and the ion cyclotron resonance. The Poisson equation is solved at each time step with the use of a method based on the fast Fourier transform. The code is written in Fortran 90 and is parallelized with the use of OpenMP directives.Comparison is performed with a real experiment with protein cytochrome c. The effect of coalescence of spectral peaks is demonstrated at high charge densities in the case of three masses.