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Table 5 A bistable biochemical network with multiple timescales and spontaneous escape

From: Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Reactions

Kinetics

Reactions

Kinetics

S1 + P → S1:P

k1

→ Ef

k4

S2 + P → S2:P

k1

Ef

k5

S3 + P → S3:P

k1

→ Ef

k6

S4 + P → S4:P

k1

Ef

k7

S1:P + S2:P → S1:P2:S2

k1

Ef + P → Ef:P

k8

S1:P + S3:P → S1:P2:S3

k1

Ef:P → Ef + P

k-8

S1:P + S4:P → S1:P2:S4

k1

Ef:P → Ef + P*

k8cat

S2:P + S3:P → S2:P2:S3

k1

Eb + P → Eb:P

k9

S2:P + S4:P → S2:P2:S4

k1

Eb:P → Eb + P

k-9

S3:P + S4:P → S3:P2:S4

k1

Eb:P → Eb + P*

k9cat

S1:P → S1 + P

k-1

P:O + RNAP → P:O:RNAP

k10

S2:P → S2 + P

k-1

P:O:RNAP → P:O + RNAP

k-10

S3:P → S3 + P

k-1

P:O:RNAP → P:O + RNAP:DNA

k11

S4:P → S4 + P

k-1

P:O + (S1:P2:S2)3→ P:O*

k12

S1:P2:S2 → S1:P + S2:P

k-1

P:O* → P:O + (S1:P2:S2)3

k-12

S1:P2:S3 → S1:P + S3:P

k-1

P:O* + RNAP → P:O*:RNAP

k13

S1:P2:S4 → S1:P + S4:P

k-1

P:O*:RNAP → P:O* + RNAP

k-13

S2:P2:S3 → S2:P + S3:P

k-1

P:O*:RNAP → P:O* + RNAP:DNA

k14

S2:P2:S4 → S2:P + S4:P

k-1

RNAP:DNA → RNAP + mRNA

k15, N15

S3:P2:S4 → S3:P + S4:P

k-1

mRNA + Rib → Rib:mRNA

k16

2 S1:P2:S2 → (S1:P2:S2)2

k2

Rib:mRNA → mRNA+Rib:mRNA1

k17

S1:P2:S2 + (S1:P2:S2)2→ (S1:P2:S2)3

k3

Rib:mRNA1 → Rib + P

k18, N18

(S1:P2:S2)2→ 2 S1:P2:S2

k-2

mRNA →

k19

(S1:P2:S2)3→ S1:P2:S2 + (S1:P2:S2)2

k-3

P →

k20

Rate Laws & Kinetic Constants:

0th order: k6 = 200 [molecules/sec]

1st order: k-1 = 50, k-2 = k-3 = 0.2, k7 = 3.5, k-8 = k-9 = 1, k8cat = 150, k9cat = 50, k-10 = k-13 = 0.1, k11 = 0.01, k-12 = 1.155e-3, k14 = 0.2, k17 = 33, k19 = 2.31e-3, k20 = 1.1155e-3 [1/sec]

2nd order: k1 = 0.025, k2 = 1e-3, k3 = 1e-5, k4 = 0.015 (mono-molecular), k8 = 2.5e-4, k9 = 8.47e-5, k10 = 0.05, k12 = 0.01, k13 = 0.1, k16 = 5e-3 [molecules sec]-1

3rd order: k5 = 1e-4 (mono-molecular) [molecules2 sec]-1

Gamma-distributed events: k15 = 30 nt/sec, N15 = 1200 nt, k18 = 33 aa/sec, N18 = 400 aa

Initial Conditions: #Po = #P* o = 4000, #S1o = #S2o = #S3o = #S4o = 1500, #Ribo = 300, #RNAPo = 180, #Efo = #Ebo = 250, otherwise 0 [Molecules]

  1. The computational times of a large-scale system benchmark using the fixed Euler-Maruyama (EM) and Milstein implementations of the HyJCMSS algorithm and the Next Reaction variant of the stochastic simulation algorithm (SSA). ND: Not Determined