Loop Dynamics in DNA Denaturation
نویسندگان
چکیده
منابع مشابه
Macroscopic loop formation in circular DNA denaturation.
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture simil...
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We present detailed molecular dynamics results for the displacement autocor-relation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is smaller than, or exceeds the correlation length. In the first case, the spectra are dominated by a single peak, whose frequency approaches the bare acoustic fre...
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Gaining knowledge and understanding of the structure and function of DNA, our genetic material, is crucial for dealing with diseases related to DNA. In 2004, the mapping of the complete human genome was accomplished, leading to an enormous progress in treating DNA-related diseases. The attention was for a long time directed at the DNA structure, specifically the sequence. However, the knowledge...
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We briefly review some of the models used to describe DNA denaturation dynamics, focusing on the value of the dynamical exponent z, which governs the scaling of the characteristic time τ ∼ L as a function of the sequence length L. The models contain different degrees of simplifications, in particular sometimes they do not include a description for helical entanglement: we discuss how this aspec...
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The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect this symmetry. Linking dissipation via untwist is allowed only at the two ends of the double strand. The result is a slow denaturation characterized by two ti...
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ژورنال
عنوان ژورنال: Physical Review Letters
سال: 2007
ISSN: 0031-9007,1079-7114
DOI: 10.1103/physrevlett.98.038103