2012/08/09 by R. Tapia-Rojo, Rafael Tapia‐Rojo, Diego Prada‐Gracia +3
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Base pair #Biology #Brownian motion #Chain (unit) #Computational biology #DNA #DNA and Nucleic Acid Chemistry #DNA sequencing #Diffusion and Search Dynamics #Energy (signal processing) #Energy landscape #Evolutionary biology #Gene #Genetics #Genome #Mesoscopic physics #Physics #Protein Structure and Dynamics #Quantum mechanics #Sequence (biology) #Statistical physics #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1103/physreve.86.021908
published as Physical Review E 86, 021908 (2012) · 7 pages, 5 figures, 1 table
openalex publication_date 2012/08/09 · arxiv created 2012/08/20 · arxiv updated 2012/08/21 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.