High-precision dosimetry - Revision history

IlinaMediaWiki at 17:29, 2 September 2014

2014-09-02T17:29:45Z

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	* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Simulated are 6109 DNA pairs with the following structures: double helix, nucleosome, chromatine fibres, chromatine fibre loops and chromosome territories. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step.		* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Simulated are 6109 DNA pairs with the following structures: double helix, nucleosome, chromatine fibres, chromatine fibre loops and chromosome territories. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step.

-	* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output is dose deposited in the cell cytoplasm and in the cell nucleus.	+	* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output among other things is the dose deposited in the cell cytoplasm and in the cell nucleus.

	== <span style="color:#000080"> How to run the tutorial </span> ==		== <span style="color:#000080"> How to run the tutorial </span> ==

IlinaMediaWiki at 16:17, 2 September 2014

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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	The macro microbeam.mac produces root files '''microbeam_t0.root''' and ''microbeam_t1.root''' with ntuples grouped in five folders.	+	The macro microbeam.mac produces root files '''microbeam_t0.root''' and '''microbeam_t1.root''' with ntuples grouped in five folders.

-	You can analyze the root ~~files~~ using '''plot.C''' macro.	+	You can analyze the root ntuples using the '''plot.C''' macro.

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">

IlinaMediaWiki at 16:16, 2 September 2014

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	* step length [nm]		* step length [nm]
	* kinetic energy difference along the step [eV]		* kinetic energy difference along the step [eV]
		+
		+	You can open the first root file and see the different ntuples:
		+
		+	<pre style="color: #800000; background-color: #dcdcdc">
		+	[username@plus1 dnaphysics_build]$ root -l dna_t0.root
		+
		+	root [1] new TBrowser
		+
		+	Select ROOT Files, dna_t0.root and Folder dna
		+
		+	Click on the different leafs
		+	</pre>

	You can analyze the root files using '''plot.C''' macro.		You can analyze the root files using '''plot.C''' macro.
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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	The macro dnageometry.mac produces a root ~~files~~ '''dnageometry.root''' with ntuples ~~containing the following~~ information for those steps ~~with a~~ deposited energy in the DNA backbone different from zero:	+	The macro dnageometry.mac produces a root file '''dnageometry.root''' with ntuples. The ntuples contain information for those geant4 steps for which the deposited energy in the DNA backbone is different from zero:

	* type of particle		* type of particle
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	</pre>		</pre>

-	The macro produces a plot that shows the position of the two DNA strands ~~shown~~ in two ~~different~~ colors. The spheres represent the amino bases. ~~Keep in mind that the~~ plot shows only the DNA pairs with ~~the~~ deposited energy (see ~~how~~ the ~~ntuples are defined~~ in SteppingAction.cc).	+	The macro produces a plot that shows the position of the two DNA strands in two colors. The spheres represent the amino bases. The plot shows only the DNA pairs with deposited energy (see the ntuple deffinition in SteppingAction.cc).

	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png
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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	~~====~~ <~~span~~ style="color:#~~000080~~"> ~~Run with different settings~~ </~~span~~> ~~====~~	+	The macro microbeam.mac produces root files '''microbeam_t0.root''' and ''microbeam_t1.root''' with ntuples grouped in five folders.
		+
		+	You can analyze the root files using '''plot.C''' macro.
		+
		+	<pre style="color: #800000; background-color: #dcdcdc">
		+	[username@plus1 dnaphysics_build]$ root -l
		+
		+	root [1] .x plot.C
		+	</pre>
		+
		+	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/microbeam/plot.png

	== <span style="color:#000080"> Files </span> ==		== <span style="color:#000080"> Files </span> ==

	[[List of high-precision dosimetry files with brief description]]		[[List of high-precision dosimetry files with brief description]]

IlinaMediaWiki at 15:42, 2 September 2014

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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for steps with a deposited energy in the DNA backbone different from zero:	+	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for those steps with a deposited energy in the DNA backbone different from zero:

	* type of particle		* type of particle

IlinaMediaWiki at 13:49, 2 September 2014

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	==== <span style="color:#000080"> Run with different settings </span> ====		==== <span style="color:#000080"> Run with different settings </span> ====
		+
		+	== <span style="color:#000080"> Files </span> ==
		+
		+	[[List of high-precision dosimetry files with brief description]]

IlinaMediaWiki at 11:17, 2 September 2014

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	* <span style="color:#ff0000"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. Simulated is a an electron beam using class '''G4ParticleGun'''. The beam is shot from the center of the cube. The output of this tutorial is a root ntuple with type of particle, type of physics process, energy deposit, energy loss and step length for every simulation step.		* <span style="color:#ff0000"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. Simulated is a an electron beam using class '''G4ParticleGun'''. The beam is shot from the center of the cube. The output of this tutorial is a root ntuple with type of particle, type of physics process, energy deposit, energy loss and step length for every simulation step.

-	* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step.	+	* <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Simulated are 6109 DNA pairs with the following structures: double helix, nucleosome, chromatine fibres, chromatine fibre loops and chromosome territories. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step.

	* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output is dose deposited in the cell cytoplasm and in the cell nucleus.		* <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output is dose deposited in the cell cytoplasm and in the cell nucleus.

IlinaMediaWiki at 10:55, 2 September 2014

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	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png

-	You can modify ~~the~~ root macro '''plot.C''' and plot the other ntuples.	+	You can modify root macro '''plot.C''' and plot the other ntuples.

	=== <span style="color:#ff0000"> microbeam </span> ===		=== <span style="color:#ff0000"> microbeam </span> ===

IlinaMediaWiki at 10:51, 2 September 2014

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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for ~~step~~ with a deposited energy different from zero:	+	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for steps with a deposited energy in the DNA backbone different from zero:

	* type of particle		* type of particle

IlinaMediaWiki at 10:34, 2 September 2014

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	==== <span style="color:#000080"> Root file </span> ====		==== <span style="color:#000080"> Root file </span> ====

-	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for ~~every~~ step:	+	The macro dnageometry.mac produces a root files '''dnageometry.root''' with ntuples containing the following information for step with a deposited energy different from zero:

	* type of particle		* type of particle

IlinaMediaWiki at 10:31, 2 September 2014

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	</pre>		</pre>

-	The macro produces a plot that shows the position of the two DNA strands:	+	The macro produces a plot that shows the position of the two DNA strands shown in two different colors. The spheres represent the amino bases. Keep in mind that the plot shows only the DNA pairs with the deposited energy (see how the ntuples are defined in SteppingAction.cc).

	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png