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

Ida Friis, Alexey Verkhovtsev, Ilia A. Solov'yov*, Andrey V. Solov'yov

*Kontaktforfatter for dette arbejde

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Abstrakt

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.

OriginalsprogEngelsk
TidsskriftJournal of Computational Chemistry
Vol/bind41
Udgave nummer28
Sider (fra-til)2429-2439
ISSN0192-8651
DOI
StatusUdgivet - 30. okt. 2020

Fingeraftryk Dyk ned i forskningsemnerne om 'Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field'. Sammen danner de et unikt fingeraftryk.

Citationsformater