The Geant4-DNA project

The Geant4-DNA project proposes to develop an open-source simulation software based and fully included in the general-purpose Geant4 Monte Carlo simulation toolkit. The main objective of this software is to simulate biological damages induced by ionising radiation at the cellular and sub-cellular scale. This project was originally initiated by the European Space Agency for the prediction of deleterious effects of radiation that may affect astronauts during future long duration space exploration missions. In this paper, the Geant4-DNA collaboration presents an overview of the whole ongoing project, including its most recent developments already available in the last Geant4 public release (9.3 BETA), as well as an illustration example simulating the direct irradiation of a chromatin fibre. Expected extensions involving several research domains, such as particle physics, chemistry and cellular and molecular biology, within a fully interdiciplinary activity of the Geant4 collaboration are also discussed.Comment: presented by S. Incerti at the ASIA SIMULATION CONFERENCE 2009, October 7-9, 2009, Ritsumeikan University, Shiga, Japa

Geant4 physics processes for microdosimetry simulation: design foundation and implementation of the first set of models

New physical processes specific for microdosimetry simulation are under development in the Geant4 Low Energy Electromagnetic package. The first set of models implemented for this purpose cover the interactions of electrons, protons and light ions in liquid water; they address a physics domain relevant to the simulation of radiation effects in biological systems, where water represents an important component. The design developed for effectively handling particle interactions down to a low energy scale and the physics models implemented in the first public release of the software are described

Models of biological effects of radiation in the Geant4 toolkit

A project, named Geant4-DNA, is in progress to extend the Geant4 simulation toolkit to model the effects of radiation with biological systems at cellular and DNA level. The first component implemented in the first development cycle of the project describes the fractional survival of a population of cells irradiated with photons or charged particles. The software system developed provides the user the option to choose among a small set of alternative models for the calculation of mammalian cell survival after irradiation. The flexible design adopted makes the system open to further extension to implement other cell survival models available in literature. The preliminary design of a prototype of the cell survival models implemented and preliminary results in some selected cell lines are described

The combination of quantitative faecal occult blood test and faecal calprotectin is a cost-effective strategy to avoid colonoscopies in symptomatic patients without relevant pathology

Background: Faecal occult blood test (FOBT) has demonstrated effectiveness in colorectal cancer (CRC) screening. Faecal calprotectin (FC) has proven efficient for evaluating activity in inflammatory bowel disease (IBD), but its value in CRC detection is less established. Most symptomatic patients have benign pathologies, but still undergo colonoscopy in many settings. Aims: To evaluate the diagnostic accuracy and cost-effectiveness of the combination of FOBT plus FC in symptomatic patients. Methods: Patients who completed colonic investigations and returned stool samples, on which FOBT and FC were performed, were recruited prospectively. CRC, advanced adenoma, IBD and angiodysplasia were considered as relevant pathologies. Results: A total of 404 patients were included, of whom 87 (21.5%) had relevant pathologies. Sensitivity and specificity were 50.6% and 69.6% for FOBT, 78.2% and 54.4% for FC. Negative predictive value (NPV) was 90.1% for FC and 86.9% for FOBT. NPV for the combination of FOBT and FC was 94.1%, with a sensitivity and specificity of 88.5% and 50.3%. The area under ROC (receiver operator curve) (AUC) was 0.741 for FOBT, 0.736 for FC and 0.816 for the combination. The total cost for visits and procedures was €233, 016 (€577/patient). Using a combination of FOBT and FC as pre-endoscopic tool allows colonoscopies to be reduced by 39.4%, reducing total costs by 20.5%. Conclusion: The combination of FOBT and FC has a better diagnostic accuracy compared with each test alone. Performing both tests before colonoscopy is a less costly and more effective strategy, reducing unnecessary procedures and complications

Validation of Geant4 atomic relaxation against the NIST Physical Reference Data

The accuracy of the Geant4 component for the simulation of atomic relaxation has been evaluated against the experimental measurements of the NIST Standard Reference Data. The validation study concerns X-ray andAuger transition energies. The comparison of the simulated and experimental data with rigorous statistical methods demonstrates the excellent accuracy of the simulation of atomic de-excitation in Geant4

Geant4 Atomic Relaxation

The Low Energy Electromagnetic package of the Geant4 toolkit incorporates a component for the simulation of atomic relaxation of elements with atomic number between 6 and 100. This process is triggered by the creation of a vacancy in the atomic shell occupancy as a result of an incident particle interaction with an atom of the target material. X-ray fluorescence and Auger electron emission result from the relaxation cascade. The availability of a model handling the atomic relaxation in Geant4 extends the applicability of the simulation toolkit to experimental use cases concerning the investigation of material properties through their characteristic X-ray or Auger emission. It is also relevant to precise simulation applications, like microdosimetry or the design and optimization of detectors based on nanotechnology. The key features of the software development process, the software architecture and design, and the implementation details of the physics model are described