Table 1.

Most widely used radiation transport and track-structure Monte Carlo (MC) codes for the simulation of radiation-induced damage.

Code	Particles	Pros	Cons	Ref.
EGS4	photons & e-	Developed specifically for dose calculations in RT applications	Not applicable at the nanoscale due to limitations of the physics models	[47]
FLUKA	Large set of particles	Multipurpose code covering medical, space, nuclear, and high-energy applications	Closed-source code. Not applicable at the nanoscale due to limitations of the physics models	[48,49]
Geant4	large set of particles	Open-source toolkit covering medical, space, nuclear, and high-energy applications. Contains powerful visualization packages. Includes low-energy physics models for sub-keV transport. Maintained by a large international collaboration	Complex toolkit. Computationally intensive. Requires users with advanced programming skills.	[41,50]
Geant4-DNA	Large set of particles	Performs event-by-event simulation for track-structure applications in liquid water. Includes a variety of low-energy electron models. Includes chemistry (water radiolysis) and biology (DNA damage and repair models) Maintained by a large international collaboration and continuously upgraded	Complex toolkit. Computationally intensive. Requires users with advanced programming skills.	[51,52]
KURBUC	Photons, neutrons, electrons, protons, alpha, carbon ions	Performs event-by-event simulations down to very low energies for track-structure applications. Includes physics models for both gaseous and liquid water medium. Includes chemistry (water radiolysis) and biology (DNA damage and repair models)	Proprietary code. Specific to water medium.	[53,54]
MC4	e-, protons, α-particles	Performs event-by-event simulations down to low-energies for track-structure applications. Includes physics models for both gaseous and liquid water medium. Known for its upgraded models for the liquid phase.	Proprietary code. Specific to water. Does not extend to relativistic energies.	[55,56,57,58]
MCDS	e-, p, alpha particles & ions	Simulates in a very fast way (ranging from seconds to minutes) the induction and clustering of DNA lesions.	Lacks accuracy. Impossible to generate damage configurations for e- with energy lower than 80 eV.	[59]
MCNP	Large set of particles	Multipurpose code covering nuclear and medical applications. Known for its accurate neutron models.	Not a free access code.	[60]
PARTRAC	e- & ions	Performs event-by-event simulation for track-structure applications. Uses physics models specifically developed for liquid water. Includes chemistry (water radiolysis) and biology (DNA damage and repair models)	Proprietary code. Specific to water. Does not include relativistic energies. The parameterization of the DNA model does not consider the DNA atomic composition.	[17,61]
PENELOPE	Photons, e- & e+	Developed for dose calculations in radiotherapy applications. Known for its electron models that extend to low-energies. Event-by-event simulations possible for application to microdosimetry	Limited track-structure applications due the incomplete simulation of electron track ends. Requires users with advanced programming skills to develop their own applications.	[62]
PEREGRINE	Large set of particles	Developed for radiotherapy treatment planning.	Gives results through a computer cluster. Not applicable at the nanoscale due to limitations of the physics models	[63]
RITRACKS	e- & ions	Performs event-by-event simulation up to relativistic energies. Simulation of radiation tracks without the need of extensive knowledge of computer programming. Simple in use.	Distributed only to authorized users. Specific to water. Uses atomic cross sections that are not reliable for nanoscale transport in liquid water.	[64]
Topas-nBio	large set of particles	Uses Geant4-DNA as its transport engine. Simply to use software specifically developed for radiobiological applications at the (sub) cellular level.	Not (yet) open-sourced. Specific to water medium.	[65]
TRAX	e- & ions	Performs event-by-event simulation for track-structure applications in various media.	Uses atomic cross sections that are not reliable for nanoscale transport in condensed-phase media.	[66]