Physica D 177 (2003) 233–241 Revisiting Salerno’s sine-Gordon model of DNA: active regions and robustness Erik Lennholm a , Michael Hörnquist b,∗ a Department of Physics and Measurement Technology, Linköping University, S-581 83 Linköping, Sweden b Department of Science and Technology, Linköping University, S-601 74 Norrköping, Sweden Received 5 July 2002; received in revised form 22 October 2002; accepted 15 November 2002 Communicated by C.K.R.T. Jones Abstract 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. © 2002 Elsevier Science B.V. All rights reserved. PACS: 66.90.+r; 87.10.+e; 87.15.He; 63.20.Ry Keywords: Sine-Gordon; DNA; Genome-wide; Robustness; Promoters 1. Introduction During the last decade, much effort has been put into simple dynamical models of DNA. Although the real DNA molecule offers an overwhelmingly complexity, it appears that certain distinct effects, such as denaturation, might be quite accurately described within the framework of very simple models [1]. The value of these models lies in the fact that if we can describe the outcome of certain experiments on the DNA molecule by just considering, e.g., one degree of freedom per base-pair, then we can draw the conclusion that this variable is the relevant one for the process under study [2]. For example, both the model by Peyrard and Bishop [3] and the model by Causo et al. [4] have showed remarkable correspondences with real denaturation experiment, showing explicitly the relevance of simple models of complex molecules [5,6]. One of the first simple mathematical models of DNA was proposed by Englander et al. [7], in which the molecule is modelled by a discrete chain of pendula, mathematically described by the sine-Gordon equation. A simple but ∗ Corresponding author. Tel.: +46-11-363381; fax: +46-11-363270. E-mail addresses: erile@ifm.liu.se (E. Lennholm), micho@itn.liu.se (M. Hörnquist). 0167-2789/02/$ – see front matter © 2002 Elsevier Science B.V. All rights reserved. PII:S0167-2789(02)00769-8