Bubbles, Clusters and Denaturation in Genomic DNA: Modeling, Parametrization, Efficient Computation
نویسندگان
چکیده
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for relevant statistical mechanics. Computed melting profiles long short heterogeneous sequences are presented, using a recently reparametrization PBD model, critically discussed. statistics extended open bubbles bound clusters formulated results presented selected examples.
منابع مشابه
Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrizat...
متن کاملBubbles and denaturation in DNA.
The local opening of DNA is an intriguing phenomenon from a statistical-physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code cannot take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological op...
متن کاملDNA denaturation bubbles at criticality.
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over fewer than ten base pairs are associated with much larger free energies of formation per site than...
متن کاملQuantifying supercoiling-induced denaturation bubbles in DNA
In both eukaryotic and prokaryotic DNA sequences of 30–100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive sin...
متن کاملDenaturation Bubbles in Fluctuating Dna Chains
– A statistical model of DNA, coupling base pair states (unbroken or broken) and thermal chain fluctuations, is formulated and then investigated using an exact solution obtained by transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length are deduced. Novel results include (i) the melting temperature emerges nat...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Nonlinear Mathematical Physics
سال: 2021
ISSN: ['1776-0852', '1402-9251']
DOI: https://doi.org/10.1142/s1402925111001611