Monte carlo damage simulation (mcds) software brain anoxia

Monte carlo damage simulation (MCDS) software


D. Stewart, ph.D.; associate professor of radiation oncology

School of medicine,

Department of radiation oncology,

1959 NE pacific street, seattle, WA 98195

Results from the MCDS have been cited in at least 41 peer-reviewed studies and 2 book


In a 2012

Red journal paper by frese et al.2012, the MCDS was used in combination with the

Repair-misrepair-fixation ( RMF) model to predict

Spatial variations in the relative biological

Effectiveness (RBE) of protons and carbon ions in representative spreadout bragg peaks (SOBP). See also

RD stewart,

Models and mechanisms

Connecting physics and biology at multiple scales in the biological hierarchy

(presented at the 2014 AAPM meeting in austin, TX, TU-A-BRE-3, july 22, 2014;

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Abstract #23482) for interesting background information and some of the theory

Behind the MCDS + RMF approach to modeling RBE effects.


Many decades of biophysical research provide evidence suggesting that

The number and spatial arrangement of energy deposits within and near

The DNA produce many types of clustered DNA lesion, including single

Strand breaks (SSB), double strand breaks (DSB) and clusters of damaged

Bases. Through a breakage and reunion process, double strand breaks

(DSB) are converted to small- and larger-scale chromosomal exchanges

With the potential to cause phenotypic alterations, neoplasia and cell

Death (see an idealized schematic showing time

Scales and selected events in radiation damage to cells and tissues).Brain anoxia

Other types of non-DSB cluster may also have significant biological

Consequences. As the only method currently available to determine the

Number and spatial configuration of lesions forming a cluster, monte

Carlo simulations are a potentially useful adjunct to experiments

Probing the underlying basis for the effects of oxygen and radiation

Quality on cell death. Estimates of DSB yields from monte carlo

Simulations can also be used in combination with kinetic reaction-rate

Models, such as the repair-misrepair-fixation (RMF) model ( carlson

Et al. 2008), to determine the relative biological

Effectiveness (RBE) for cell killing of different types of radiation.

An improved understanding of RBE and oxygen effects are needed to more

brain anoxia

Fully exploit the biological potential of protons and carbon ions in

Radiation therapy, especially as high levels of pre-treatment tumor

Hypoxia have been implicated as a significant factor contributing to

Treatment failure.

General features of the MCDS


The original MCDS (semenenko and stewart 2004,

2006) simulates the induction and

Clustering of DNA lesions in normoxic cells (O 2 concentrations greater than about 21%) uniformly

Irradiated by monoenergetic electrons, protons and a particles with energies as

High as 1 gev. In the latest version of MCDS ( stewart

Et al. 2011), the allowed particle types have been expanded to include

Ions up to and including 56 fe. The allowed range of particle energies has been

brain anoxia

Expanded ( see table), and the induction of damage for

Arbitrary mixtures of charged particles with the same or different kinetic

Energies can be directly simulated. Cluster yields for photons and other

Neutral particles can be computed for the distribution of secondary charged

Particles produced in monolayer cell or other geometries (e.G., see

Hsiao and stewart 2008). Although not

Required for the simulation of damage induction, the MCDS reports information

Such as the charged particle stopping power in water, CSDA range, absorbed dose

Per unit fluence, frequency-mean specific energy, energy imparted per radiation

Event, and the lineal energy.

Software availability an

Executable of MCDS software (version 3.10A, compiled december 5, 2011) for MS windows

brain anoxia

And linux is

Freely available for commercial, educational or research purposes (see below). An executable of MCDS 2.01 (march 2006) is also available (see also the

MCDS 2.01 website). Inquiries

About the MCDS program and related publications or software should be directed to

Dr. Rob stewart.

• download MCDS 2.01

(march 2006 distribution) as a 200 kbyte zip file

• download MCDS 3.00B (july

25, 2011 distribution) as a 456 kbyte zip file

• download MCDS 3.10A (compiled december 5, 2011)

• executable for MS windows ( 631

Kbyte zip file)

• executable for linux ( 363

Kbyte zip file) — see linux


• see also the readme1st.Txt and

How2run.Txt files

Sample input output files

The MCDS reads particle and other simulation information

brain anoxia

From an ASCII input file(s) and then writes the results of the simulation to

Another ASCII (output) file. For neutral particles (e.G.,

G-rays from 60co

And 137cs) and for mixtures of

Different types of charged particles, the main input file (e.G.,

60Co.Inp) must include a line that

Points to the name of a secondary data file (e.G.,

60Co.Dat). The .Dat file

Specifies the types, energy and relative weight ( fluence) to use to

Simulate a mixed radiation field.

• 1 gev proton (100% O 2): input ( proton1.Inp)

And output file ( proton1.Out)

• 1 gev proton (0% O 2): input ( proton2.Inp)

And output file ( proton2.Out)

• 60 co

(100% O 2 ): input

Files ( 60co.Inp

And 60co.Dat) and output file ( 60co.Out)

• 137 cs

(100% O 2): input ( 137cs.Inp

brain anoxia

And 137cs.Dat) and output file ( 137cs.Out)

• 125 I

(100% O 2): input ( 125I.Inp

And 125I.Dat) and output file ( 125I.Out)


Many additional input and output files are included in the software



X dose tallies in

MCNP 6.1 ( and


A useful, and

Computationally very efficient, method to compute RBE-weighted dose in MCNP

(or MCNPX) is to modify a standard (so-called F6) dose tally in

MCNP by a user-defined dose-response function (DE DF option). Below are links to some examples of MCNP tallies to record RBE weighted

Dose for the endpoint of DSB induction in well oxygenated and anoxic cells

(links are to an ASCII file). The

RBE dose-response function (DE DF card) is based on 60co

G-rays as the reference radiation, i.E., 8.3

brain anoxia

DSB gy -1 gbp -1 for well oxygenated cells and 2.86 DSB gy -1

Gbp -1 for anoxic cells ( stewart

Et al. 2011,

Kirkby et al. 2013). See also

Stewart et al., rapid MCNP simulation of DNA double

Strand break (DSB) relative biological effectiveness (RBE) for photons,

Neutrons, and light ions, phys. Med. Biol.



Electron RBE (10 ev to 1 gev )

· 1H + RBE

(1 kev to 1 gev )

· 2H + RBE

(1 kev to 1 gev )

· 3H + RBE (1 kev to 1

GeV )

· 3he 2+ RBE (1 kev to 1

GeV )

· 4he 2+ RBE (1 kev to 1

GeV )

In addition to sample dose tallies modified by the RBE for DSB induction, the

Above examples also includes tallies to record LET x dose, the frequency-mean

Specific energy (5 um biological target) x dose, and the mean specific energy

brain anoxia

Times the square of the number of DSB gy -1 gbp -1. The latter quantity is useful for estimating the RBE for reproductive

Cell death using the repair-misrepair-fixation (RMF) model ( carlson

Et al. 2008), i.E., the linear quadratic (LQ) model parameters are

Approximately equal to





K z F S 2




K S 2/2

( carlson et al. 2008,

Frese et al. 2012).





Are are cell- and tissue- (or tumor-) specific adjustable ( fitted)

Parameters that are independent of LET (as a first approximation), z F

Is the frequency-mean specific energy (in gy), and


Is the average number of DSB gy -1

Gbp -1

As computed with the MCDS version 3.10A.

NOTE: similar

RBE x dose tallies can (could be) easily implemented in other monte carlo code

brain anoxia

Systems (TOPAS\geant4, egsnrc, PENELOPE, FLUKA, …)

Last updated:

October 17, 2016