Improved integrated nucleus-nucleus inelastic cross sections for light nuclides in Geant4

We propose a new root-mean-square radius parameterization for light nuclei A 30 suitable for use in Geant4 calculations of nucleus-nucleus total hadronic inelastic scattering cross sections. The new approach takes into account the proton-neutron asymmetry of the reactants, and was fit to 360 measured total inelastic cross sections from the EXFOR database. Measured nuclear radii are better described in the new approach than the current Geant4 implementation, particularly for unstable nuclides, and there is better agreement with measured cross sections for both stable and unstable nuclides. The improved parameterization should help in carbon-ion therapy applications in particular.This work was supported by the Australian Research Council under Grants DP170102423 and DP170100967

Effects of loading a magnetic field longitudinal to the linear particle-beam track on yields of reactive oxygen species in water

The effects of a magnetic field longitudinal to the ion beam track on the generation of hydroxyl radicals (•OH) and hydrogen peroxide (H2O2) in water were investigated. A longitudinal magnetic field was reported to enhance the biological effects of the ion beam. However, the mechanism of the increased cell death by a longitudinal magnetic field has not been clarified. The local density of •OH generation was estimated by a method based on the EPR spin-trapping. A series of reaction mixtures containing varying concentrations (0.76‒2278 mM) of DMPO was irradiated by 16 Gy of carbon- or iron-ion beams at the Heavy-Ion Medical Accelerator in Chiba (HIMAC, NIRS/QST, Chiba, Japan) with or without a longitudinal magnetic field (0.0, 0.3, or 0.6 T). The DMPO-OH yield in the sample solutions was measured by X-band EPR and plotted versus DMPO density. O2-dependent and O2-independent H2O2 yields were measured. An aliquot of ultra-pure water was irradiated by carbon-ion beams with or without a longitudinal magnetic field. Irradiation experiments were performed under air or hypoxic conditions. H2O2 generation in irradiated water samples was quantified by an EPR spin-trapping, which measures •OH synthesized from H2O2 by UVB irradiation. Relatively sparse •OH generation caused by particle beams in water were not affected by loading a magnetic field on the beam track. O2-dependent H2O2 generation decreased and oxygen-independent H2O2 generation increased after loading a magnetic field parallel to the beam track. Loading a magnetic field to the beam track made •OH generation denser or made dense •OH more reactive

Simulation of DNA damage using the “molecularDNA” example application of Geant4-DNA

The scientific community has a large interest in the studies of DNA damage and response after exposure to ionizing radiation. Several in-silico methods have been proposed so far to model and study the mechanisms of DNA damage using Monte Carlo simulations. The “molecularDNA” example is one of the most recent applications to simulate the irradiation of human cancer cells and bacteria using Geant4-DNA. This example enables the simulation of the physical, physico-chemical and chemical stages of liquid water irradiation, including radiolytic processes following the particle irradiation of the pre-defined human cell geometries and it can be used to calculate the early direct and non-direct DNA damage such as single (SSB) and double strand breaks (DSB) as well as DNA fragment distribution. The application is user friendly and can be used following simple macro commands. The results of the Monte Carlo simulation are compared to experimental data of DSB yields, as well as with previously published simulation data.ICCBIKG 2023 : 2nd International Conference on Chemo and Bioinformatics, September 28-29, 2023; Kragujeva

Simulation of DNA damage using Geant4-DNA: an overview of the “molecularDNA” example application

Purpose The scientific community shows great interest in the study of DNA damage induction, DNA damage repair, and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in silico methods have been proposed so far to study these mechanisms using Monte Carlo simulations. This study outlines a Geant4-DNA example application, named “molecularDNA”, publicly released in the 11.1 version of Geant4 (December 2022). Methods It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. The example includes two different DNA-scale geometries of biological targets, namely “cylinders” and “human cell”. This public version is based on a previous prototype and includes new features, such as: the adoption of a new approach for the modeling of the chemical stage, the use of the standard DNA damage format to describe radiation-induced DNA damage, and upgraded computational tools to estimate DNA damage response. Results Simulation data in terms of single-strand break and double-strand break yields were produced using each of the available geometries. The results were compared with the literature, to validate the example, producing less than 5% difference in all cases. Conclusion: “molecularDNA” is a prototype tool that can be applied in a wide variety of radiobiology studies, providing the scientific community with an open-access base for DNA damage quantification calculations. New DNA and cell geometries for the “molecularDNA” example will be included in future versions of Geant4-DNA

Evaluation of ionizing radiation induced DNA damage on a cell nucleus by integrated track structure Monte Carlo simulations using Geant4-DNA

Introduction: Monte Carlo (MC) mechanistic simulations are a promising tool for the modeling of early DNA damage induction by ionizing radiation. They allow to simulate not only physical interactions but also chemical processes in combination with sim- plified geometries of biological targets for the prediction of such damage. In the last decades, several MC codes were developed to predict DNA damage, like KURBUC PARTRAC and Geant4-DNA. Recently, Geant4-DNA has demonstrated the possibility to evaluate early DNA damage in an E. coli bacterium and in a fibroblast cell nucleus irradiated by protons [4]. We have presented for the first time the combination of such features (physics, chemistry and biological geometry) in a single Geant4-DNA application for the modelling of early DNA damage induction in a cell nucleus [5]. In this talk, we present progress of the modelling in Geant4-DNA of biological DNA damage. Material and Methods: As used in the previous work, we built fractal based cell nucleus geometry composed by double-helix DNA fiber and histone. We simulated physical particle transportation followed by radiolysis chemical product productions, diffusion of free radicals and chemical reactions in gamma and proton radiation fields. Early DNA damage is calculated as either direct damage or indirect damage. Then the damage clusters are classified according to the damage type definition proposed by Nikjoo. Results: In this talk, mainly DSB yields and fraction of indirect damage and biological repair will be presented. For instance, the simulated repair prediction shows a good agreement with experimental data. Conclusion: We have developed for the first time a Monte Carlo simulation based on Geant4-DNA that calculates not only early DNA damage but also late DNA damage prediction such as foci accumulation like γH2AX.Mini- Micro- Nano- Dosimetry (MMND)-Innovative Technologies in Radiation Oncology (ITRO) 202

Measurements of azimuthal correlation between jets and charged particles at LHC-ALICE experiment

In the nature around us, quarks and gluons are confined in hadrons due to "confinement of quarks". However, the coupling strength of the QCD between quarks and gluons is to be asymptotically weaker with the increasing their energy. At high temperature the quarks and gluons move freely beyond the boundary of hadrons. Such high energy state is called Quark-Gluon Plasma(QGP). To create such state on the earth, the ultra relativistic heavy ion collision is unique tool. It has been observed several signatures of the QGP formation at the Relativistic Heavy Ion Collider(RHIC). Suppression of high momentum particles is one of the signatures. High momentum particles are known to be produced in characteristic phenomena, jet , where high momentum particle are produced in cluster. The jet is produced when parton in each projectile is scattered with large momentum, followed by fragmentation into many hadrons. It is considered that the cause of the suppression of high momentum particle is due to the characteristic energy loss of the parton in the QGP. On the other hands, many low momentum particles are formed at characteristic energy loss and the additional instead large angles from original low momentum particles is often called modification of jet. In theoretical approach, the energy loss and the shape modification of the jet is strongly relate to properties of hot/dense matter particularly gluon density and initial temperature of the QGP. Therefore study of jet modification is a good tool to investigate the properties of the QGP. Experimentally it is very important to measure the energy loss together with the energy re-distribution at large angles. At the RHIC, it is difficult to collect enough data because of its low rate. The production cross-section of jet is strongly related to the collision energy. The Large Hadron Collider(LHC) starts nuclear-nuclear collisions with highest energy from 2010. LHC provides good opportunity to study the jet physics in heavy ion collisions to investigate parton interaction between jets and the QGP with higher statistics. Former study of the jet physics in heavy ion collisions has been done at the LHC by CMS. They have suggested the existence of re-distributed particles at large angles. In their study, the information of the spread angle is minimum and they can not see detail of jet modification. In this paper, a new analysis method is proposed in order to see the modified energy(or momentum) with the spread angle. Proposed new method handles the momentum weighted azimuthal distribution of the associate particles with respect to the leading jet and direct comparison of pp and Pb-Pb collisions have been done. In this thesis, the centrality dependence and the leading jet momentum dependence are shown to extract jet modification effects, which shed light on the knowledge of the pass length dependence of jet modification. We observe that the low momentum particles are re-distributed at large angles in the away-side of the jet with respect to the leading jet. This feature is consistent with CMS results. Furthermore we see the re-distributed momentum in the near-side. The missing momentum and the re-distributed momentum is found to be almost balanced. We see jet modification is larger with the highest jet momentum, and the effect is also larger in the central compared with peripheral collisions