Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations
Fig 2
A continuous-time discrete Markov chain model for multiple RPA molecules binding to long ssDNA.
The possible steps in the biomolecular kinetics of multiple RPA molecules binding to ssDNA. The RPA in the free solution can bind to ssDNA with rate k1 provided there are at least 20 nucleotides (nt) of consecutive unoccupied sites. This bound “20nt mode” RPA unbinds with rate k−1. When space permits, the 20nt-mode RPA can extend and bind an additional 10nt of DNA at a rate of k2, converting it to a 30nt-mode bound protein. The 30nt-mode RPA transforms back to 20nt-mode spontaneously with the rate k−2. However, when the gap is not large enough to accommodate the RPA, the binding or conversion is prohibited ( and
).