Revisiting Salerno’s sine-Gordon model of DNA: active regions and robustness

We return to a simple model of DNA-transcription, first investigated by Salerno more than 10 years ago. One conjecture that time was that the promoter-regions were “dynamically active” in the sense that a stationary kink solution to the discrete sine-Gordon equation spontaneously starts to move when positioned in certain regions. Here we explore the whole genome of the bacteriophage T7, which is the same that was used in the first studies. We find that the regions in the promoters where the DNA-binding molecules attach have no special significance, while the start of the RNA-coding regions are dynamically active on a significant level. The results are checked to be robust by imposing an external disturbance in the form of a thermostat, simulating a constant temperature.