TOPAS-nBio v4.1.0

This version brings Topas-nBio up to date for compatibility with Geant4-DNA v11.3.2+

• Fix: inconsistencies in screen output when reporting damage using the plasmid DNA example
• Fix: improved consistency in background reactions at contact
• Fix: reduced loop in map checking for finding particle names modified: processes/TsIRTConfiguration.cc modified: processes/TsIRTConfiguration.hh
• Fix: changes for builging in Geant4-DNA v11.3.2
  New nomenclature of Geant4-DNA caused incompatiblity in molecule naming,
  a map to translate names was added
• Fix: screen printing reactions happened multiple times due to double declaration of pointers of TsIRTConfiguration
• Fix: Caught several bugs
  • ResampleReactantsPosition- potential crash in zero-diffusion cases is fixed. For that, early-return added
    for D1 == 0 or D2 == 0 prevent divide-by-zero/NaNs.
  • Conversion in background contact reaction is fixed. Concentration is now multiplied by Avogadro*1e-24
  • Added a guard for type II/IV diffusion-limit. In ResolveReactionParameters (around lines ~481–497), now sim aborts
    with a descriptive message when kobs >= kdiff (preventing infinite kact/bad probabilities).
  • Misleading “Re-set charge” in printing logs. At processes/TsIRTConfiguration.cc:101-108, the message prints the
    radius instead of the charge when overriding Mo/*/Charge.
  • GetH2SO4ComponentsConcentrationP out-of-bounds risk is fixed. Previously the loop iterated
    over map Result and accessesed Result[i+1] without bounds check (~lines 970–975).

TOPAS-nBio v4.0.1

Patch for TOPAS-nBio v4.0.1

• Renamed the "master" branch to "main", and added branch "develop" for user contributions
• Added protection to avoid using Continuous mode in non-compatible scorers, fix Issue #93
• Fixes rundemos.csh reported in Discussions #105, and small mention of DBSCAN for Dnadamage with geometries in #21
• Added new tests to rundemos.csh
  • TsIRTGvalue.txt
  • TsIRTInterTrack.txt
  • TsIRTCummulative.txt
  • TemperatureExample_90C.txt
  • TsIRTAndGillespieGvalue.txt
• Restored missing scorer "simpleSSBandDSBwithDBSCAN" from previous release
• Enhanced compatability with TsIRTManager for
• TsIRT.cc
• TsScoreWithIRTCummulative.cc

TOPAS-nBio v4.0

The TOPAS-nBio Collaboration

We are pleased to announce the release of TOPAS-nBio v4.0! This release includes changes to various chemistry processes, new features, bug fixes, and updated regression tests. Further details can be found below.

We’d also like to once again thank all users for their feedback, contributions, and continued support in improving TOPAS-nBio! Your engagement helps us identify issues, implement new features, and ensure that TOPAS-nBio remains a valuable resource.

Release Notes

Processes

• Several new classes have been added:

  • For simulating the transport of lithium ions with energies below 1 MeV/u: TsDNAChargeDecrease/Increase, TsDNAKRIonBornExcitationModel, TsDNAKRIonIonisationScaledModel, TsDNAKRIonMillerGreenExcitationModel, TsDNAKondoRamosLiChargeDecrease/Increase
  • For simulating homogenous (long-time) chemistry: TsGillespie, TsIRTManager, TsVIRTProcedure, TsIRTContinuous, TsScoreWithIRTAndGillespieContinuous.

• The following classes are unnecessary due to new chemistry based on IRT, thus have been removed: TsEmDNAChemistryExtended, TsEmStandardPhysics_option4, TsH2O2, TsHO2, TsO2, TsScoreSimpleSSBandDSBWithDBSCAN

• Charge exchange processes for lithium ions have been implemented into the code. See the relevant publication: https://doi.org/10.1088/1361-6560/ad5f72

• The following improvements reconciled simulated and measured chemical yields at low LET radiation: the RMS displacement of water molecules after an ionization/excitation was set to 0.775 nm (TsDNAWaterDissociationDisplacer), and the physico-chemical branching ratios were updated (TsEmDNAChemistry).

• Improvements to the Independent Reaction Time (IRT):

  • The computation efficiency of the IRT was improved through changes implemented in TsIRTConfiguration and TsIRT. For impact on computation times see the relevant publication: https://doi.org/10.1088/1361-6560/ad5f72
  • A new IRT method called continuous IRT was implemented into this release. This application allows users to simulate the dose and dose rate dependency of long-term chemistry for continuous and quasi-continuous beam structures. See the relevant publication: https://doi.org/10.1088/1361-6560/ad9ce2
  • For the independent reaction times method, the reaction rate constant of chemical reactions between the same reactants is now input as 2k, in line with the observed reaction rate definition. Users should specify this reaction rate in their parameter files.
  • Type 5 reactions no longer need to be specified in the parameter file when the observed reaction rate is available. The observed reaction rate, which already includes spin effects, is now used in the chemistry examples. Note, however, that users can still assign a reaction type of 5 to a reaction should they so wish.

• Step-By-Step (SBS):

  • The following change is only applicable to users using the SBS with TsEmDNAChemistry. As opposed to the IRT, which is our own implementation, we are still using the SBS from Geant4. Geant4 chooses to handle the 2k multiplication internally (see the G4DNAMolecularReactionTable class), and so for reactions between the same reactants, users should provide k and not 2k in the parameter files. See the GvalueRevisedPhysicsChemistry.txt example for the appropriate chemistry parameters to use.

Examples

• Updated the readme for the CellsWithNanoparticles example.

• Fixed wrong parameter name found in GvalueRevisedPhysicsChemistry.txt and updated reaction types in TOPASDefaultReactions.txt

• Fixed the simulation setup for GvalueG4DNADefault.txt, it now gives correct yields

• FrickeIRT: Added EnableHighTimeScavenger and ELSEPA. Reaction rates/types were updated in TOPASDefaultReactions, and TOPASFrickeReactions.

• SBSGetGValue: updated reactionType

• IRTCummulative: Added ELSEPA

• IRTDamageToDNAPlasmid: changed k -> 2k and removed reactionType=5

• IRTGetGvalue: Added Meesungnoen model for the thermalization distance of solvated electrons, fixed diffusion coefficients, changed k->2k for OH+OH reaction.

• IRTInterTrack: Fixed diffusion coefficients, changed k->2k for OH+OH reaction.

• IRTTemperature: Fixed diffusion coefficients, changed k->2k for OH+OH reaction.

• ParticleTuple: Updated diffusion coefficients, reaction rates, added ELSEPA

• The TsFiber geometry component is not supported anymore, instead use TsDNAFabric; as a result the DNAFiber.txt example was removed.

• A Lithium ion example has been added for charge exchange processes. To use this example unzip the G4LithiumFiles.zip and move the files according to the instructions in the README. Please take note of the fact that directory paths might be slightly different depending on your operating system.

Bug Fixes

• Cell Culture simulations would sometimes hang in an infinite loop. This has now been fixed.

• ReportMoleculesNamed was working incorrectly and is now fixed.

• Fixed a bug in the SDD scorer where one strand break too many was being added.

New TOPAS-nBio features

• A new folder has been added called userContributions. The nanoparticle example and corresponding source code have been moved here. If you would like to share your TOPAS-nBio extensions, please don’t hesitate to reach out.

• The following parameters allow users to choose which IRT modality they want to use in their simulation:

    s:Ch/TOPASChemistry/IRTProcedure = "continuous" or,
    s:Ch/TOPASChemistry/IRTProcedure = "pure"
  

• Users can now select different branching ratio models. The default branching ratios are specified by "topasnbio", "g4dna" explicitly uses the branching ratios from Geant4-DNA, and "experimental" can be used if you are interested in testing different ratios. The experimental branching ratios can be modified in TsEmDNAChemistry.cc. After doing so don’t forget to re-build and install TOPAS-nBio:

    s:Ch/TOPASChemistry/BranchingRatiosModel = "topasnbio" or,
    s:Ch/TOPASChemistry/BranchingRatiosModel = "g4dna" or,
    s:Ch/TOPASChemistry/BranchingRatiosModel = "experimental"
  

• New parameter to select different chemistry algorithms. Parameter values "G4IRT", "G4StepByStep" (default), or "G4IRTSync" can be used.

    s:Ch/RegisterTimeStepModel = "G4IRT"
  

TOPAS-nBio v3.0

The TOPAS-nBio Collaboration.

Release notes June 3, 2024.

TOPAS-nBio v3.0 includes the first release of qc-nbio-testsuite, a continuous integration test suit for assisting user’s benchmarks and new adds to TOPAS-nBio. Additionally, results from a comprehensive regression test for accuracy evaluation are provided in a PDF document. The current release is only compatible with OpenTOPAS v.4.0 (https://opentopas.github.io/) build on top of Geant4/Geant4-DNA v11.1.3.

Details in TOPAS-nBio v3.0 accuracy can be found at the regression system

Processes.

• TsDNAWaterDissociationDisplacer::GetProductsDisplacement()
  -- The adjustable displacement parameters of water dissociations have been changed (3 Rs -> 2 Rs).
  -- The displacement of B1A1 dissociation H2O->H2+2OH has been changed consistent with momentum conservation.

• TsDNAELSEPAElasticModel
  -- TsDNAELSEPAElasticModel from G4DNAELSEPAElasticModel has been implemented with some changes in order to use density-scaling.

• TsIRT::contactReactions
  -- A double sampling of contact reactions has been corrected.
  -- The boundary condition of contact reaction is now based on reactionRadius instead of effectiveReactionRadius.

• TsIRTConfiguration::SampleIRTPartiallyDiffusionControlled()
  -- Sampling partially diffusion-controlled reactions for type II and type IV reactions now uses the acceptance-rejection method instead of the Brents function.

• TsIRTConfiguration::ResolveRemainerReactionParameters()
  -- Calculation of reaction velocity v and effectivetildeReactionRadius σ_eff^'' has been corrected.

• TsIRTConfiguration::CalculateContactProbabilities()
  -- The reaction probabilities of partially diffusion-controlled reactions have been corrected.

• TsIRTConfiguration::ContactFirstOrderAndBackgroundReactions()
  -- The contact first order reaction has been rewritten for the correct unit.
  -- The reaction radius for the contact first-order reaction is left to further discussion.

• IRT: Reaction rates and diffusion scale automatically by setting the temperature in Celsius (unitless). Water density scaling must be set manually.

• TsIRT::TsIRT()
  -- Corrected the default time steps for G-value scoring from 0.1 ps to 1 ps. This was causing the first bin of G-value to always be 0
  -- First implementation of physical processes for interactions with gold material. It only supports electrons and gammas.
  -- It can be activated with

  s:Ph/Default/Modules = 1 “TsEmDNAPhysics”
  b:Ph/Default/PhysicsForGold/Active = “True”
  s:Ph/Default/PhysicsForGold/Region = “MyRegion”
  

Scorers.

• scorers/TsScoreClusterSizeInRandomCylinders.cc/hh
  -- New ionization detail scorer for the calculation of cluster size. Generates a .phsp file with 4 columns of data containing the cluster size, ionization cluster frequency, excitation cluster frequency, and total cluster frequency

• scorers/IRTTemperature/
  -- G-value calculation in pure liquid water with temperature variation from 20 C to 90 C

• TsScoreClusterSizeInRandomCylinders::TsScoreClusterSizeInRandomCylinders()
  -- Added support for single volumes

• A new example for process in Gold: examples/processes/GoldNanoParticle.txt

• Updated DAMARIS for TOPAS-nBio 3.0