def CCOB():
mectitle = 'C-C-O-B'
ratetitle = 'quasi random numbers'
ARSB = dcpyps.State('B', 'AR*B', 0.0)
ARS = dcpyps.State('A', 'AR*', 50e-12)
AR = dcpyps.State('B', 'AR', 0.0)
R = dcpyps.State('C', 'R', 0.0)
RateList = [
dcpyps.Rate(15000.0, AR, ARS, name='beta', limits=[1e-15, 1e+7]),
dcpyps.Rate(500.0, ARS, AR, name='alpha', limits=[1e-15, 1e+7]),
dcpyps.Rate(2000.0, AR, R, name='koff', limits=[1e-15, 1e+7]),
dcpyps.Rate(5.0e08, R, AR, name='kon', eff='c', limits=[1e-15, 1e+10]),
dcpyps.Rate(9.0e07,
ARS,
ARSB,
name='kBon',
eff='c',
limits=[1e-15, 1e+10]),
dcpyps.Rate(90000.0, ARSB, ARS, name='kBoff', limits=[1e-15, 1e+7])
]
return dcpyps.Mechanism(RateList, mtitle=mectitle, rtitle=ratetitle)
def CH82():
mectitle = 'CH82'
ratetitle = 'CH82 numerical example'
A2RS = dcpyps.State('A', 'A2R*', 60e-12)
ARS = dcpyps.State('A', 'AR*', 60e-12)
A2R = dcpyps.State('B', 'A2R', 0.0)
AR = dcpyps.State('B', 'AR', 0.0)
R = dcpyps.State('C', 'R', 0.0)
RateList = [
dcpyps.Rate(15.0, AR, ARS, name='beta1', limits=[1e-15, 1e+7]),
dcpyps.Rate(15000.0, A2R, A2RS, name='beta2', limits=[1e-15, 1e+7]),
dcpyps.Rate(3000.0, ARS, AR, name='alpha1', limits=[1e-15, 1e+7]),
dcpyps.Rate(500.0, A2RS, A2R, name='alpha2', limits=[1e-15, 1e+7]),
dcpyps.Rate(2000.0, AR, R, name='k(-1)', limits=[1e-15, 1e+7]),
dcpyps.Rate(2 * 2000.0, A2R, AR, name='2k(-2)', limits=[1e-15, 1e+7]),
dcpyps.Rate(2 * 5.0e07,
R,
AR,
name='2k(+1)',
eff='c',
limits=[1e-15, 1e+10]),
dcpyps.Rate(5.0e08,
ARS,
A2RS,
name='k*(+2)',
eff='c',
fixed=True,
limits=[1e-15, 1e+10]),
dcpyps.Rate(5.0e08,
AR,
A2R,
name='k(+2)',
eff='c',
limits=[1e-15, 1e+10]),
#dcpyps.Rate(2 * 1.0 / 3.0, A2RS, ARS, name='k*(-2)', limits=[1e-15,1e+7])
dcpyps.Rate(0.66667,
A2RS,
ARS,
name='2k*(-2)',
mr=True,
limits=[1e-15, 1e+7])
]
CycleList = [dcpyps.Cycle(['A2R*', 'AR*', 'AR', 'A2R'], ['A2R*', 'AR*'])]
fastblk = False
KBlk = 0.001
return dcpyps.Mechanism(RateList,
CycleList,
mtitle=mectitle,
rtitle=ratetitle) #, fastblk, KBlk)
def CO():
mectitle = 'C-O'
ratetitle = 'quasi random numbers'
RS = dcpyps.State('A', 'O', 50e-12)
R = dcpyps.State('B', 'C', 0.0)
RateList = [
dcpyps.Rate(20.0, R, RS, name='beta', limits=[1e-15, 1e+7]),
dcpyps.Rate(50.0, RS, R, name='alpha', limits=[1e-15, 1e+7]),
]
return dcpyps.Mechanism(RateList, mtitle=mectitle, rtitle=ratetitle)
def fully_connected_cycle():
mectitle = 'Fully connected cycle'
ratetitle = 'JP numbers'
O2 = dcpyps.State('A', 'O2', 60e-12)
O1 = dcpyps.State('A', 'O1', 60e-12)
C2 = dcpyps.State('B', 'C2', 0.0)
C1 = dcpyps.State('C', 'C1', 0.0)
KC, tKO, KO = 1.0, 0.05, 5.0
k12, k13, k14 = 1.2, 1.3, 1.4
k23, k24, k34 = 2.3, 2.4, 3.4
RateList = [
dcpyps.Rate(k12, C1, C2, name='k12', eff='c', limits=[1e-15, 1e+7]),
dcpyps.Rate(k12 / KC, C2, C1, name='k21', limits=[1e-15, 1e+7]),
dcpyps.Rate(k24 / KC, C2, O2, name='k24', limits=[1e-15, 1e+7]),
dcpyps.Rate(k24 / KO, O2, C2, name='k42', limits=[1e-15, 1e+7]),
dcpyps.Rate(k34 / KO, O2, O1, name='k34', limits=[1e-15, 1e+7]),
dcpyps.Rate(k34 / tKO,
O1,
O2,
name='k43',
eff='c',
limits=[1e-15, 1e+7]),
dcpyps.Rate(k13 / tKO, O1, C1, name='k13', limits=[1e-15, 1e+10]),
dcpyps.Rate(k13, C1, O1, name='k31', limits=[1e-15, 1e+10]),
dcpyps.Rate(k14, C1, O2, name='k14', eff='c', limits=[1e-15, 1e+10]),
dcpyps.Rate(k14 / KO, O2, C1, name='k41', limits=[1e-15, 1e+7]),
dcpyps.Rate(k23 / KC, C2, O1, name='k23', limits=[1e-15, 1e+7]),
dcpyps.Rate(k23 / tKO,
O1,
C2,
name='k32',
eff='c',
limits=[1e-15, 1e+10]),
]
CycleList = [
dcpyps.Cycle(['C1', 'C2', 'O2'], ['C2', 'O2']),
dcpyps.Cycle(['C2', 'O2', 'O1'], ['O2', 'O1']),
dcpyps.Cycle(['C1', 'C2', 'O1'], ['C1', 'O1']),
]
return dcpyps.Mechanism(RateList,
CycleList,
mtitle=mectitle,
rtitle=ratetitle)
def six_cycles_mec():
mectitle = 'six cycles'
ratetitle = 'quasi random numbers'
A = dcpyps.State('A', 'A', 60e-12)
B = dcpyps.State('A', 'B', 60e-12)
C = dcpyps.State('A', 'C', 60e-12)
D = dcpyps.State('B', 'D', 60e-12)
E = dcpyps.State('B', 'E', 0.0)
F = dcpyps.State('B', 'F', 0.0)
G = dcpyps.State('B', 'G', 0.0)
H = dcpyps.State('B', 'H', 0.0)
I = dcpyps.State('B', 'I', 0.0)
J = dcpyps.State('B', 'J', 0.0)
K = dcpyps.State('B', 'K', 0.0)
L = dcpyps.State('C', 'L', 0.0)
RateList = [
dcpyps.Rate(15.0, A, B, name='ab'),
dcpyps.Rate(25.0, B, A, name='ba'),
dcpyps.Rate(15.0, A, E, name='ae'),
dcpyps.Rate(25.0, E, A, name='ea'),
dcpyps.Rate(15.0, B, C, name='bc'),
dcpyps.Rate(25.0, C, B, name='cb'),
dcpyps.Rate(15.0, B, F, name='bf'),
dcpyps.Rate(25.0, F, B, name='fb'),
dcpyps.Rate(15.0, C, D, name='cd'),
dcpyps.Rate(25.0, D, C, name='dc'),
dcpyps.Rate(15.0, C, G, name='cg'),
dcpyps.Rate(25.0, G, C, name='gc'),
dcpyps.Rate(15.0, D, H, name='dh'),
dcpyps.Rate(25.0, H, D, name='hd'),
dcpyps.Rate(15.0, E, F, name='ef'),
dcpyps.Rate(25.0, F, E, name='fe'),
dcpyps.Rate(15.0, E, I, name='ei'),
dcpyps.Rate(25.0, I, E, name='ie'),
dcpyps.Rate(15.0, F, G, name='fg'),
dcpyps.Rate(25.0, G, F, name='gf'),
dcpyps.Rate(15.0, F, J, name='fj'),
dcpyps.Rate(25.0, J, F, name='jf'),
dcpyps.Rate(15.0, G, H, name='gh'),
dcpyps.Rate(25.0, H, G, name='hg'),
dcpyps.Rate(15.0, G, K, name='gk'),
dcpyps.Rate(25.0, K, G, name='kg'),
dcpyps.Rate(15.0, H, L, name='hl'),
dcpyps.Rate(25.0, L, H, name='lh'),
dcpyps.Rate(15.0, I, J, name='ij'),
dcpyps.Rate(25.0, J, I, name='ji'),
dcpyps.Rate(15.0, J, K, name='jk'),
dcpyps.Rate(25.0, K, J, name='kj'),
dcpyps.Rate(15.0, K, L, name='kl'),
dcpyps.Rate(25.0, L, K, name='lk')
]
return dcpyps.Mechanism(RateList, mtitle=mectitle, rtitle=ratetitle)