Parameter study (cylinders.mac)
Table of contents
Overview
The simulation geometry is based upon a past parameter study [1] of direct and indirect DNA damage yields in straight DNA fibres to study the impacts of the different parameters. The cylinders.mac macro file can be used for such simulation.
Geometry
The geometry for parameter sweeps consists of a 3 μm sphere filled with 200.000 individual 216 bp long straight DNA segments in a 100 nm × 30 nm × 30 nm placement volume. Radical kill distance Damage model is set to 9 nm and the range for direct interaction is set to 7 A.
/world/worldSize 10200 nm
/cell/radiusSize 3 3 3 um
/scheduler/endTime 1 us
/dnageom/setSmartVoxels 1
/dnageom/checkOverlaps false
/dnageom/radicalKillDistance 9 nm
/dnageom/interactionDirectRange 7 angstrom
/dnageom/placementSize 30 30 100 nm
/dnageom/fractalScaling 1 1 1 nm
/dnageom/definitionFile geometries/prisms200k_r3000.txt
/dnageom/placementVolume prism geometries/straight-216-0.txt
/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false
/dnageom/useCustomMoleculeSizes false
A spherical chromosome named “cylinder” is defined for analysis using:
/chromosome/add cylinder sphere 3000 0 0 0 nm
Particle source
Primary electrons are generated randomly, with a random direction in a smaller 500 nm sphere in the centre of the test region. The primary particles with energies no greater than 4.5 keV cannot escape the larger spherical region, and all primaries see an equivalently random region.
/gps/particle e-
/gps/ang/type iso
/gps/energy 4.5 keV
/gps/pos/type Volume
/gps/pos/shape Sphere
/gps/pos/radius 500 nm
/gps/pos/centre 0 0 0 nm
/run/beamOn 100000
Damage model
Direct damage model uses the 17.5 eV for lower and upper break thresholds.
/dnadamage/directDamageLower 17.5 eV
/dnadamage/directDamageUpper 17.5 eV
/dnadamage/indirectOHBaseChance 1.0
/dnadamage/indirectOHStrandChance 0.65
/dnadamage/inductionOHChance 0.0
/dnadamage/indirectHBaseChance 1.0
/dnadamage/indirectHStrandChance 0.65
/dnadamage/inductionHChance 0.0
/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.65
/dnadamage/inductionEaqChance 0.0
Results
Output (see analysis) is analysed by using the cylinders.C ROOT macro file.
Refer classification model for detail of source and complexity frequency.
Visualization
For visualization, the following line can be used:
/control/execute vis.mac
More specifically, start moleculardna using the command:
./molecular
to open the Qt visualiser. Then use the mac file that you want, e.g.
/control/execute cylinders.mac
For such visualization, a large amount of RAM is needed. For example using cylinders DNA geometries, to visualize 200 cylinders, ~2.5 Gb are needed. For 2000 cylinders, ~11 Gb are needed.
References
[1] Computational modelling of lowenergy electron-induced DNA damage by early physical and chemical events, H. Nikjoo et al., Int. J. Radiat. Biol. 71 (1997) 467–483 - link