Can one predict DNA Transcription Start Sites by studying bubbles?
  It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated. 
Titus S. van Erp, Santiago Cuesta-Lopez, Johannes-Geert Hagmann and   Michel Peyrard