Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile
Fig 4
Density and current profiles numerically computed via stochastic simulations (blue and magenta dots, respectively) and analytically estimated (black lines) for and L = 1: (a, b) LD:
= 0.2,
= 1; (c, d) HD:
= 1,
= 0.2; (e, f) MC:
= 1,
= 1.
Hopping and drop-off events are scheduled based on the Gillespie algorithm [41]. All simulations, here and in the following, are for 107 iteration steps (each iteration corresponds to one reaction: initiation, elongation, drop-off or termination). The first 2 ⋅ 107 iterations were discarded to make sure that the system was in a steady state. Unless otherwise stated, a lattice size of 500 sites was used.