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molecularDNA

Parameter study (cylinders.mac)

Table of contents

  1. Parameter study (cylinders.mac)
    1. Overview
    2. Geometry
    3. Particle source
    4. Damage model
    5. Results
    6. Visualization
    7. Reference

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.

Geometry

The geometry for parameter sweeps consists of a 3 μm sphere filled with 200.000 individual 216bp long straight DNA segments in a 100×30×30 nm placement volume. Radical kill distance Damage model was set to 9 nm, as well as the range for direct interaction was 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 6.5 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

cylinders

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 0.00

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.65
/dnadamage/inductionEaqChance 0.00

Results

Output (see analysis) is analysed by using cylinders.C macro file.

cylinders

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, 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.

Reference

  1. Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events, Nikjoo et al.,Int. J. Rad. Bio., 1997, 71, 467.