The incipient denaturation mechanism of DNA
M Xu, T Dai, Y Wang, G Yang - RSC advances, 2022 - pubs.rsc.org
DNA denaturation is related to many important biological phenomena, such as its
replication, transcription and the interaction with some specific proteins for single-stranded …
replication, transcription and the interaction with some specific proteins for single-stranded …
Large bubble drives circular DNA melting
S Sengupta, SM Bhattacharjee, G Mishra - Physical Chemistry …, 2024 - pubs.rsc.org
We investigate the melting transition of non-supercoiled circular DNA of different lengths,
employing Brownian dynamics simulations. In the absence of supercoiling, we find that …
employing Brownian dynamics simulations. In the absence of supercoiling, we find that …
Large bubble drives melting in circular DNA
S Sengupta, SM Bhattacharjee, G Mishra - arXiv preprint arXiv …, 2024 - arxiv.org
We investigate the melting transition of non-supercoiled circular DNA of different lengths,
employing Brownian dynamics simulation. In the absence of supercoiling, we find that …
employing Brownian dynamics simulation. In the absence of supercoiling, we find that …
Hotter isn't faster for a melting RNA hairpin
We investigate the denaturation dynamics of nucleic acids through extensive molecular
dynamics simulations of a coarse-grained RNA hairpin model. In apparent contradiction with …
dynamics simulations of a coarse-grained RNA hairpin model. In apparent contradiction with …
[HTML][HTML] Generalized Poland–Scheraga denaturation model and two-dimensional renewal processes
G Giacomin, M Khatib - Stochastic Processes and their Applications, 2017 - Elsevier
Abstract The Poland–Scheraga model describes the denaturation transition of two
complementary–in particular, equally long–strands of DNA, and it has enjoyed a remarkable …
complementary–in particular, equally long–strands of DNA, and it has enjoyed a remarkable …
DNA melting structures in the generalized Poland-Scheraga model
Q Berger, G Giacomin, M Khatib - arXiv preprint arXiv:1703.10343, 2017 - arxiv.org
The Poland-Scheraga model for DNA denaturation, besides playing a central role in
applications, has been widely studied in the physical and mathematical literature over the …
applications, has been widely studied in the physical and mathematical literature over the …
Denaturation of circular DNA: supercoils and overtwist
The denaturation transition of circular DNA is studied within a Poland-Scheraga-type
approach, generalized to account for the fact that the total linking number (LK), which …
approach, generalized to account for the fact that the total linking number (LK), which …
MODELING DNA THERMAL DENATURATION AT THE MESOSCOPIC LEVEL.
M Dolfin, M Lachowicz - Discrete & Continuous Dynamical …, 2014 - search.ebscohost.com
In this paper a mesoscopic approach is proposed to describe the process of breaking of
hydrogen bonds during the DNA thermal denaturation, also known as DNA melting. A …
hydrogen bonds during the DNA thermal denaturation, also known as DNA melting. A …
Models of DNA denaturation dynamics: universal properties
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 …
focusing on the value of the dynamical exponent $ z $, which governs the scaling of the …
THE GENERALIZED POLAND-SCHERAGA MODEL: A BIVARIATE RENEWAL APPROACH TO DNA DENATURATION
M Khatib - 2016 - theses.hal.science
The Poland-Scheraga (PS) model is the standard basic model to study the denaturation
transition of two complementary and equally long strands of DNA. This model has enjoyed a …
transition of two complementary and equally long strands of DNA. This model has enjoyed a …