Modeling the effect of ion‐induced shock waves and DNA breakage with the reactive CHARMM force field

Ion‐induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated how single‐ and double strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to: (a) quantify the shock wave propagation and (b) describe the dynamics of formation of DNA breaks. The article concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation set‐ups. When biological material is irradiated with ions, they create a “hot” cylinder of rapidly moving water molecules around their trajectories, effectively inducing shock waves. This induced shock wave may potentially cause DNA strand breaks when the wave front hits the molecule. Here the computational foundation for modeling this effect is described in detail, especially how to calculate and implement the reactive CHARMM force field.