Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. The adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions to the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.

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Recent developments in GEANT4

Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit

This Special Report presents a description of Geant4-DNA user applications dedicated to the simulation of track structures (TS) in liquid water and associated physical quantities (e.g., range, stopping power, mean free path…). These example applications are included in the Geant4 Monte Carlo toolkit and are available in open access. Each application is described and comparisons to recent international recommendations are shown (e.g., ICRU, MIRD), when available. The influence of physics models available in Geant4-DNA for the simulation of electron interactions in liquid water is discussed. Thanks to these applications, the authors show that the most recent sets of physics models available in Geant4-DNA (the so-called "option4" and "option 6" sets) enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquid water, than the default set of models ("option 2") initially provided in Geant4-DNA. They also serve as reference applications for Geant4-DNA users interested in TS simulations.

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Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project.

In the current opinion, we would like to study adhesion of DNA and RNA−amphiphile complexes to non–modified glasses, glasses containing phenylboronic acid (PBA) attached via 3– glycidoxypropyltrimethoxysilane (GPTMS) [(PBA–GPTMS–glasses)] and glasses containing grafted dimethyllacrylamide–acrylamide phenylboronic acid (DMAA–AAPBA) copolymer (DMAA–AAPBA– glasses). We prepared glasses modified with GPTMS and then attached PBA to them. After that, we modified glasses by (3–mercaptoropyl) trimethoxy silane (MPTMS) and grafted DMAA–AAPBA copolymer to the modified glass plates. For increasing the measuring sensitivity, DNA and RNA−amphiphile complexes were stained with Procion Red HE3B, Red 4GE, Red 510, Red KE3B, Red 120, Red ABO, Red A4G, Red 3B, Red KE3B, Red HE3G, Red 53 L, Red HE3BI, Red E3B, Red CT3B, Red ES3B, Red LHE3B, Red I3B, Red HE3BFC, Red MEB, Red SE3BI, Red 24990, Red SE3B, Red 3BHE and other active and reactive dyes. DNA and RNA−amphiphile complexes stained with Procion Red HE3B, Red 4GE, Red 510, Red KE3B, Red 120, Red ABO, Red A4G, Red 3B, Red KE3B, Red HE3G, Red 53 L, Red HE3BI, Red E3B, Red CT3B, Red ES3B, Red LHE3B, Red I3B, Red HE3BFC, Red MEB, Red SE3BI, Red 24990, Red SE3B, Red 3BHE and other active and reactive dyes formed denser and more stable layer on the copolymer–grafted supports compared onto supports modified with phenylboric acid via a organosilane spacer [1–18]. Adhesion of DNA and RNA−amphiphile complexes to boronate–containing polymer fixed on solid support in different conditions such as pH, precipitation time and different concentrations of glucose (dextrose), fructose (levulose) and galactose were studied.

A Thermodynamic Study on Hydration and Dehydration of DNA and RNA Amphiphile Complexes

The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.

https://bioone.org/journals/radiation-research/volume-191/issue-2/RR15226.1/TOPAS-nBio--An-Extension-to-the-TOPAS-Simulation-Toolkit/10.1667/RR15226.1.pdf

TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology

An accurate modeling of radial energy deposition around ion tracks is a key requirement of radiation transport software used for simulations in radiobiology at the sub-cellular scale. The work presented in this paper is part of the on-going benchmarking of the “Geant4-DNA” physics processes and models, which are available in the Geant4 Monte Carlo simulation toolkit for the low energy transport of particles in liquid water. We present for the first time radial dose distributions of incident ion tracks simulated with “Geant4-DNA”. Simulation results are compared to other results available in the literature, obtained from analytical calculations, step-by-step Monte Carlo simulations and measurements. They show a reasonable agreement with reference data.

Q.T. Pham

Papers

Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit

Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study