ArticlePhysica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)2017
Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries.
Article in Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 83 citations in OpenAlex.
- Applications of artificial intelligence in nuclear medicine.Zeitschrift fur medizinische Physik · 2026Review
- A refined approach to compute nanodosimetric quantities for proton and ion radiotherapy treatment planning.Physics in medicine and biology · 2025Article
- High-complexity of DNA double-strand breaks is key for alternative end-joining choice.Communications biology · 2024Article
- Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair.Radiation research · 2023Article
- Estimation of relative biological effectiveness ofEJNMMI physics · 2023Article
- Simulation of DNA damage using Geant4-DNA: an overview of the "molecularDNA" example application.Precision radiation oncology · 2023Article
- Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA.International journal of molecular sciences · 2022Article
- Article
- Article
- The relation between microdosimetry and induction of direct damage to DNA by alpha particles.Physics in medicine and biology · 2021Article
- Evaluating very high energy electron RBE from nanodosimetric pBR322 plasmid DNA damage.Scientific reports · 2021Article
- Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage.PLoS computational biology · 2020Article
- Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio.Radiation research · 2020Article
- Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations.Cancers · 2020Review
- Intercomparison of dose enhancement ratio and secondary electron spectra for gold nanoparticles irradiated by X-rays calculated using multiple Monte Carlo simulation codes.Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) · 2020Article
- Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams.Physics in medicine and biology · 2019Article
- Clinically relevant nanodosimetric simulation of DNA damage complexity from photons and protons.RSC advances · 2019Article
- Mechanistic Modelling of Radiation Responses.Cancers · 2019Review
- TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.Radiation research · 2019Article
- A New Standard DNA Damage (SDD) Data Format.Radiation research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 1 country.
Funding
Abstract
Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can help bridge the gap between physics, chemistry and biology. The TOPAS collaboration is tackling this challenge by extending the current Monte Carlo tool to allow for sub-cellular in silico simulations in a new extension, TOPAS-nBio. TOPAS wraps and extends the Geant4 Monte Carlo simulation toolkit and the new extension allows the modeling of particles down to vibrational energies (∼2eV) within realistic biological geometries. Here we present a validation of biological geometries available in TOPAS-nBio, by comparing our results to two previously published studies. We compare the prediction of strand breaks in a simple linear DNA strand from TOPAS-nBio to a published Monte Carlo track structure simulation study. While TOPAS-nBio confirms the trend in strand break generation, it predicts a higher frequency of events below an energy of 17.5eV compared to the alternative Monte Carlo track structure study. This is due to differences in the physics models used by each code. We also compare the experimental measurement of strand breaks from incident protons in DNA plasmids to TOPAS-nBio simulations. Our results show good agreement of single and double strand breaks predicting a similar increase in the strand break yield with increasing LET.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.