public void IsomerGammaEmission(Particle p, double deltaDepth, int i)
{
Random random = new Random();
double pp = SimpleRNG.GetUniform();
if (pp < pp_IsomerGammaEmission(deltaDepth, i))
{
Particle p_gamma = new Particle(p_type.photon);
list_newParticles.Add(p_gamma);
}
}
public void NewParticles(Particle p, double deltaDepth, int i)
{
if (p.p_t != p_type.neutron || p.p_t != p_type.proton)
{
Random random = new Random();
double pp = SimpleRNG.GetUniform();
if (pp < 0.01) // improve the prob. of fragmentation
{
list_removeParticles.Add(p); // the primary disappears
int n_products = 10; // should be a random number of secondaries
for (int j = 0; j < n_products / 2; j++)
{
Particle p_born = new Particle(p_type.proton); // a constructor for a proton; later add more secondaries, like neutrons, light ions, etc.
list_newParticles.Add(p_born);
}
for (int j = 0; j < n_products / 2; j++)
{
Particle p_born = new Particle(p_type.neutron); // a constructor for a proton; later add more secondaries, like neutrons, light ions, etc.
list_newParticles.Add(p_born);
}
//double z = p.Z - 2; // crude model of fragmentation // zzz
//double e = 0.8 * p.E;
//double a = p.A - n_products / 2;
//Particle p_primary_frag;
//if (p.GetPtype(a, z, e) == p_type.not_known)
//{
// p_primary_frag = new Particle();
// p_primary_frag.Initialize(a, z, e);
//}
//else
// p_primary_frag = new Particle(p.GetPtype(a, z, e)); // primary fragment
//list_newParticles.Add(p_primary_frag);
//Particle p_target_frag = new Particle();
//p_target_frag.Initialize(14 + 13 - n_products / 2, 13 - 2, 0.2 * p.E); // give it Al A, Z, E for now // target fragment
//list_newParticles.Add(p_target_frag);
}
}
}
//
public static bool ApplyRad2RWs(RadiationSchema rs, RandomWalk rw, DSBs DSBdata)
{
int ndsb = 0;
try
{
double dose;
double dose_total = 0.0;
for (int nb = 0; nb < rs.nBeams; nb++) // iterate over all beams
{
foreach (int j in rw.nmonomer)
{
dose = Dconst;
dose_total += Dconst;
try
{
for (int i = 0; i < amorphous_partile_tracks[nb].track_struct.ntracks; i++)
{
int x = amorphous_partile_tracks[nb].track_struct.X[i];
int y = amorphous_partile_tracks[nb].track_struct.Y[i];
int dist2 = (x - rw.LL[j].X) * (x - rw.LL[j].X) + (y - rw.LL[j].Y) * (y - rw.LL[j].Y);
if (dist2 < Convert.ToInt32((RadiationSchema.Pr / lattice_dim) * (RadiationSchema.Pr / lattice_dim)))
{
int t = Convert.ToInt32(MainForm.Particle.Tracks.grid * lattice_dim * Math.Sqrt(dist2) / RadiationSchema.Pr); // microns
dose += amorphous_partile_tracks[nb].track_struct.dose[t];
dose_total += amorphous_partile_tracks[nb].track_struct.dose[t];
}
}
}
catch { return(false); }
double Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high/low LET; also 1e-5 is factored out
if (amorphous_partile_tracks[nb].p_t == MainForm.Radiation.p_type.photon)
{
Q = 0.812; // multiply by 35./25. for high LET
}
else
{
Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high LET
}
Q *= 1.0e-5; // Q is determined from PFGE experiments
Random random = new Random();
try
{
if (SimpleRNG.GetUniform() < 1.0 - Math.Exp(-Q * dose))
{
ndsb++;
DSBs.DSBstruct new_dsb = new DSBs.DSBstruct
{
ndsb = ndsb,
L = rw.LL[j],
position = rw.nmonomer[j],
entry_time = rs.entryTime[nb],
exit_time = rs.exitTime[nb]
};
new_dsb.random_time = SimpleRNG.GetUniform() * (new_dsb.exit_time - new_dsb.entry_time) + new_dsb.entry_time; // a DSB is created sometime during the fractionation interval
double r = SimpleRNG.GetUniform();
if (r < DSBs.DSBcomplP[0])
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.simpleDSB;
}
else
{
if (r >= DSBs.DSBcomplP[0] && r < DSBs.DSBcomplP[1]) // zzz can a DSB appear more than 1 time at the same monomer
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplus;
}
else
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplusplus;
}
}
DSBdata.listDSBs.Add(new_dsb);
}
}
catch { return(false); }
}
}
dose_total /= Convert.ToDouble(rw.nmonomer.Length); // total dose integrated over all monomers // zzz might wanna output somewhere
return(true);
}
catch { return(false); }
}
//
public bool RestitutionKinetics(List <Object> listObjs)
{
// the class FreeEnds is derived from DSBs class and is based on DSBdata
// Free_end class is for Objects (which are fragments that can have free ends)
Random random = new Random();
try
{
for (int i = 0; i < Convert.ToInt32(expTime / tau); i++) // number of elementary time steps
{
if (!SplitObjects(listObjs, i * tau, (i + 1) * tau))
{
return(false); // split only using DSBs avaibale in time interval timeIncrement / tau
}
int availableFreeEnds = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
availableFreeEnds++;
}
}
}
if (availableFreeEnds != 0)
{
for (int j = 0; j < availableFreeEnds / 2; j++) // cycle through all pairs of Free Ends in one elementary time step
{
int availableFreeEnds1 = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
availableFreeEnds1++; // determine the number of free ends, which are still reactive
}
}
}
int end1, end2;
while (true)
{
end1 = random.Next(0, availableFreeEnds1);
end2 = random.Next(0, availableFreeEnds1);
if (end1 != end2)
{
break;
}
}
int itemp = 0;
Free_end freeend1 = null, freeend2 = null;
foreach (Object o in listObjs)
{
bool b = false;
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
if (itemp == end1)
{
fe.Reacting = true;
freeend1 = fe;
b = true;
break;
}
itemp++;
}
}
if (b)
{
break;
}
}
itemp = 0;
foreach (Object o in listObjs)
{
bool b = false;
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
if (itemp == end2)
{
fe.Reacting = true; // this marks a free end for rejoining/misrejoining
freeend2 = fe;
b = true;
break;
}
itemp++;
}
}
if (b)
{
break;
}
}
if (freeend1 != null && freeend2 != null)
{
if (freeend1.Position == freeend2.Position) // proper ends
{
if (SimpleRNG.GetUniform() < P)
{
Object o_new = new Object();
if (CreateMergedObj(o_new, listObjs)) // merge the chosen reactive ends in the chosen objects and remove the objs with this pair of free ends
{
listObjs.Add(o_new);
// renumber bands in the whole genome
int[] b_index = new int[46];
foreach (Object o in listObjs)
{
foreach (Band b in o.md.chromo_bands)
{
b_index[b.Chromo_num]++;
b.Ordinal_number = b_index[b.Chromo_num];
}
}
}
else
{
o_new = null; // this happens when one if the members of listObjs becomes a ring
}
}
}
else
{
if (SimpleRNG.GetUniform() < MisrejoiningProb(freeend1, freeend2))
{
Object o_new = new Object();
if (CreateMergedObj(o_new, listObjs)) // merge the chosen reactive ends in the chosen objects
{
listObjs.Add(o_new);
// renumber bands in the whole genome
int[] b_index = new int[46];
foreach (Object o in listObjs)
{
foreach (Band b in o.md.chromo_bands)
{
b_index[b.Chromo_num]++;
b.Ordinal_number = b_index[b.Chromo_num];
}
}
}
else
{
o_new = null; // this happens when one if the members of listObjs becomes a ring
}
}
}
// if nothing happens de-activate free ends
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.Reacting)
{
fe.Reacting = false;
}
}
}
}
}
}
}
if (CheckDSBlist(DSBdata) && CheckObjList(listObjs))
{
return(true);
}
else
{
return(false);
}
}
catch
{ // merge failure
Detailed_checkObjList(listObjs);
Detailed_checkDSBlist(DSBdata);
return(false);
}
}