Include nucleus targeted nanoparticle models

examples/TSSphericalCellNP_geometries.topas

@@ -27,7 +27,7 @@ s:Ge/MyCell/Membrane/Material="Cytoplasm"
 s:Ge/MyCell/Membrane/Color="grass"
 s:Ge/MyCell/Membrane/DrawingStyle="wireframe"
 
-#NANOPARTICLES - optional
+#NANOPARTICLES in the cytosol - optional
 i:Ge/MyCell/Nanoparticle/NumberOfNanoparticles = 1000
 d:Ge/MyCell/Nanoparticle/r = 50 nm
 s:Ge/MyCell/Nanoparticle/Material = "Gold"

examples/TSSphericalCellNP_minimal_example.topas

@@ -69,7 +69,7 @@ s:Ge/MyCell/Membrane/Material="Cytoplasm"
 s:Ge/MyCell/Membrane/Color="grass"
 s:Ge/MyCell/Membrane/DrawingStyle="wireframe"
 
-#NANOPARTICLES - optional
+#NANOPARTICLES in the cytosol - optional
 i:Ge/MyCell/Nanoparticle/NumberOfNanoparticles = 1000
 d:Ge/MyCell/Nanoparticle/r = 50 nm
 s:Ge/MyCell/Nanoparticle/Material = "Gold"

examples/TSSphericalCellNP_targetedNP_geometries.topas

@@ -0,0 +1,44 @@
+#### CELL ####
+s:Ge/MyCell/Type="TsSphericalCellSphericalNP"
+s:Ge/MyCell/Material="Cytoplasm"
+s:Ge/MyCell/Parent="World"
+d:Ge/MyCell/CellRadius= 5.0 um
+s:Ge/MyCell/Color="white"
+
+#NUCLEUS
+d:Ge/MyCell/Nucleus/NucleusRadius= 3.0 um 
+s:Ge/MyCell/Nucleus/Material="Nucleoplasm"
+d:Ge/MyCell/Nucleus/translateX = 0.0 um
+d:Ge/MyCell/Nucleus/translateY = 0.0 um
+d:Ge/MyCell/Nucleus/translateZ = 0.0 um
+s:Ge/MyCell/Nucleus/DrawingStyle="wireframe"
+s:Ge/MyCell/Nucleus/Color="red"
+
+#MITOCHONDRIA - optional
+i:Ge/MyCell/Mitochondria/NumberOfMitochondria= 10
+d:Ge/MyCell/Mitochondria/r= 500 nm
+s:Ge/MyCell/Mitochondria/Material="Cytoplasm"
+s:Ge/MyCell/Mitochondria/Color="grass"
+s:Ge/MyCell/Mitochondria/DrawingStyle="wireframe"
+
+#MEMBRANE - optional
+d:Ge/MyCell/Membrane/Thickness = 10.0 nm
+s:Ge/MyCell/Membrane/Material="Cytoplasm"
+s:Ge/MyCell/Membrane/Color="grass"
+s:Ge/MyCell/Membrane/DrawingStyle="wireframe"
+
+#NANOPARTICLES in the cytosol - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticles = 1000
+d:Ge/MyCell/Nanoparticle/r = 50 nm
+s:Ge/MyCell/Nanoparticle/Material = "Gold"
+s:Ge/MyCell/Nanoparticle/Color = "yellow"
+s:Ge/MyCell/Nanoparticle/DrawingStyle = "solid"
+
+#NANOPARTICLES at the nucleus - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticlesAtNucleus=500
+
+#NANOPARTICLES at the mitochondria - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticlesAtMitochondria=100
+
+#The total number of nanoparticles is 1600 here
+#all with the same radius, material etc

examples/TSSphericalCellNP_targetedNP_minimal_example.topas

@@ -0,0 +1,86 @@
+#### GENERAL ####
+i:Ts/Seed =  1  #starting random seed 
+i:Ts/NumberOfThreads = -1
+b:Ts/DumpParameters = "True" 
+Ts/PauseBeforeQuit = "False"
+
+
+#### GUI ####
+s:Gr/ViewA/Type = "OpenGL"
+i:Gr/ViewA/WindowSizeX = 1200
+i:Gr/ViewA/WindowSizeY = 1000
+u:Gr/ViewA/Zoom = 2.
+Ts/UseQt = "True"
+
+#### MATERIALS #### 
+#Pure gold
+sv:Ma/Gold/Components = 1 "Gold"
+uv:Ma/Gold/Fractions = 1 1.0
+d:Ma/Gold/Density = 19.32 g/cm3
+s:Ma/Gold/DefaultColor = "yellow"
+
+#Cell cytoplasm
+sv:Ma/Cytoplasm/Components = 4 "Hydrogen" "Carbon" "Nitrogen" "Oxygen"
+uv:Ma/Cytoplasm/Fractions = 4 0.1025 0.1225 0.0425 0.7325
+d:Ma/Cytoplasm/Density = 1.0 g/cm3
+s:Ma/Cytoplasm/DefaultColor = "blue"
+
+#Cell Nucleoplasm
+sv:Ma/Nucleoplasm/Components = 6 "Hydrogen" "Carbon" "Nitrogen" "Oxygen" "Sulfur" "Potassium"
+uv:Ma/Nucleoplasm/Fractions = 6 0.106 0.09 0.032 0.742 0.004 0.026
+d:Ma/Nucleoplasm/Density = 1.0 g/cm3
+s:Ma/Nucleoplasm/DefaultColor = "red"
+
+
+#### WORLD ####
+s:Ge/World/Type = "TsBox"
+d:Ge/World/HLX = 6. um
+d:Ge/World/HLY = 6. um
+d:Ge/World/HLZ = 6. um
+s:Ge/World/Material = "Vacuum"
+
+
+#### CELL ####
+s:Ge/MyCell/Type="TsSphericalCellSphericalNP"
+s:Ge/MyCell/Material="Cytoplasm"
+s:Ge/MyCell/Parent="World"
+d:Ge/MyCell/CellRadius= 5.0 um
+s:Ge/MyCell/Color="white"
+
+#NUCLEUS
+d:Ge/MyCell/Nucleus/NucleusRadius= 3.0 um 
+s:Ge/MyCell/Nucleus/Material="Nucleoplasm"
+d:Ge/MyCell/Nucleus/translateX = 0.0 um
+d:Ge/MyCell/Nucleus/translateY = 0.0 um
+d:Ge/MyCell/Nucleus/translateZ = 0.0 um
+s:Ge/MyCell/Nucleus/DrawingStyle="solid"
+s:Ge/MyCell/Nucleus/Color="red"
+
+#MITOCHONDRIA - optional
+i:Ge/MyCell/Mitochondria/NumberOfMitochondria= 100
+d:Ge/MyCell/Mitochondria/r= 300 nm
+s:Ge/MyCell/Mitochondria/Material="Cytoplasm"
+s:Ge/MyCell/Mitochondria/Color="grass"
+s:Ge/MyCell/Mitochondria/DrawingStyle="wireframe"
+
+#MEMBRANE - optional
+d:Ge/MyCell/Membrane/Thickness = 10.0 nm
+s:Ge/MyCell/Membrane/Material="Cytoplasm"
+s:Ge/MyCell/Membrane/Color="grass"
+s:Ge/MyCell/Membrane/DrawingStyle="wireframe"
+
+#NANOPARTICLES in the cytosol - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticles = 1000
+d:Ge/MyCell/Nanoparticle/r = 50 nm
+s:Ge/MyCell/Nanoparticle/Material = "Gold"
+s:Ge/MyCell/Nanoparticle/Color = "yellow"
+s:Ge/MyCell/Nanoparticle/DrawingStyle = "solid"
+
+#NANOPARTICLES at the nucleus - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticlesAtNucleus=500
+
+#NANOPARTICLES at the mitochondria - optional
+i:Ge/MyCell/Nanoparticle/NumberOfNanoparticlesAtMitochondria=100
+
+#The total number of nanoparticles is 1600 here
+#all with the same radius, material etc