PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

Delage, Erick; Pham, Quang-Dung; Karamitros, Mathieu; Payno, H.; Štěpán, Václav; Incerti, S.; Maigne, Lydia; Perrot, Y.

doi:10.1016/j.cpc.2015.02.026

Cited by 38 publications

(35 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Users can however also model single chromatin fibers or single double helix strands. TOPAS-nBio can read in geometries from the Protein Data Bank (PDB) [13] as well as DNAFabric [14] (see Figure 1c). Although nuclear DNA is a primary radiation target, TOPAS-nBio allows other non-nuclear target sites to be modeled (e.g., mitochondria [15, 16]).…”

Section: Methodsmentioning

confidence: 99%

Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries

et al. 2017

View full text Add to dashboard Cite

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 (~ 2 eV) 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 17.5 eV 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.

show abstract

Section: Methodsmentioning

confidence: 99%

Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The efficiency with respect to N s for DSBs classified with a geometry-based algorithm [28] is shown on the left side of Figure 8. The relative efficiency ranges from a factor of 31.0 ±0.2 up to a factor 58.2 ±0.4 for N s = 128.…”

Section: Resultsmentioning

confidence: 99%

“…The Geant4 pdb2dna algorithm we used to estimate the number of DNA strand breaks was restricted to simple SSB’s and DSB’s [28]. We expect our demonstration of the performance of PST in this scenario will motivate further exploration of the capabilities of these kinds of techniques in more complex scenarios.…”

Section: Discussionmentioning

confidence: 99%

Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations

et al. 2017

View full text Add to dashboard Cite

Flagged uniform particle splitting was implemented with two methods to improve the computational efficiency of Monte Carlo track structure simulations with TOPAS-nBio by enhancing the production of secondary electrons in ionization events. In Method 1 the Geant4 kernel was modified. In Method 2 Geant4 was not modified. In both methods a unique flag number assigned to each new split electron was inherited by its progeny, permitting reclassification of the split events as if produced by independent histories. Computational efficiency and accuracy were evaluated for simulations of 0.5–20 MeV protons and 1–20 MeV/u carbon ions for three endpoints: (1) mean of the ionization cluster size distribution, (2) mean number of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) classified with DBSCAN, and (3) mean number of SSBs and DSBs classified with a geometry-based algorithm. For endpoint (1), simulation efficiency was 3 times lower when splitting electrons generated by direct ionization events of primary particles than when splitting electrons generated by the first ionization events of secondary electrons. The latter technique was selected for further investigation. The following results are for Method 2, with relative efficiencies about 4.5 times lower for Method 1. For endpoint (1), relative efficiency at 128 split electrons approached maximum, increasing with energy from 47.2±0.2 to 66.9±0.2 for protons, decreasing with energy from 51.3±0.4 to 41.7±0.2 for carbon. For endpoint (2), relative efficiency increased with energy, from 20.7±0.1 to 50.2±0.3 for protons, 15.6±0.1 to 20.2±0.1 for carbon. For endpoint (3) relative efficiency increased with energy, from 31.0±0.2 to 58.2±0.4 for protons, 23.9±0.1 to 26.2±0.2 for carbon. Simulation results with and without splitting agreed within 1% (2 standard deviations) for endpoints (1) and (2), within 2% (1 standard deviation) for endpoint (3). In conclusion, standard particle splitting variance reduction techniques can be successfully implemented in Monte Carlo track structure codes.

show abstract

“…This is described in the work of Delage et al [65] (http://pdb4dna.in2p3.fr) who developed a dedicated Geant4-DNA extended example, the so-called "pdb4dna" example. This example also includes a cross-platform C++ library of tools.…”

Section: The High-resolution Atomistic Approachmentioning

confidence: 99%

“…Figure 3. Example of irradiation of the 3BSE 16-base-pair B-DNA PDB© molecule by 10 incident 10 keV electrons, simulated with the Geant4-DNA "pdb4dna" example [65].…”

Section: The High-resolution Atomistic Approachmentioning

confidence: 99%

Review of Geant4-DNA applications for micro and nanoscale simulations

et al. 2016

Self Cite

View full text Add to dashboard Cite

Emerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-byevent electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis. Since its release, Geant4-DNA has been adopted as an investigational tool in kV and MV external beam radiotherapy, hadron therapies using protons and heavy ions, targeted therapies and radiobiology studies. It has been benchmarked with respect to other track structure Monte Carlo codes and, where available, against reference experimental measurements. While Geant4-DNA physics models and radiolysis modelling functionalities have already been described in detail in the literature, this review paper summarises and discusses a selection of representative papers with the aim of providing an overview of a) geometrical descriptions of biological targets down to the DNA size, and b) the full spectrum of current micro-and nano-scale applications of Geant4-DNA. Disciplines Engineering | Science and Technology Studies Publication DetailsIncerti, S., Douglass, M., Penfold, S., Guatelli, S. & Bezak, E. (2016). Review of Geant4-DNA applications for micro and nanoscale simulations. Physica Medica: an international journal devoted to the applications of physics to medicine and biology, 32 (10), 1187-1200. AbstractEmerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-by-event electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis.

show abstract

PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

Cited by 38 publications

References 30 publications

Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries

Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries

Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations

Review of Geant4-DNA applications for micro and nanoscale simulations

Contact Info

Product

Resources

About