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As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify all the stationary solutions of the model, as well as analytic approximations of them, both in the continuum and in the discrete limits. Our results explain the structure of the solutions reported by Theodorakopoulos {em et al.} [Phys. Rev. Lett. {bf 93}, 258101 (2004)] and provide a way to proceed to the analysis of the generalized version of the model incorporating the genetic information.
We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-th
The zinc finger structure where a Zn2+ ion binds to 4 cysteine or histidine amino acids in a tetrahedral structure is very common motif of nucleic acid binding proteins. The corresponding interaction model is present in 3% of the genes of human genom
A variety of physical, social and biological systems generate complex fluctuations with correlations across multiple time scales. In physiologic systems, these long-range correlations are altered with disease and aging. Such correlated fluctuations i
The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings--despite the fact that many bacteria inhabit complex a
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow