Related papers: Generalized Poland-Scheraga model for DNA hybridiz…
The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…
We study the dynamical behaviour of the proton transfer in the hydrogen bonds in the base-pairs of the double helices of the DNA type. Under the assumption that the elastic and the tunnelling degrees of freedom may be coupled, we derive a…
Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
The broken phase of the Next-to two-Higgs-doublet model (N2HDM) constitutes an archetype of extended Higgs sectors. In the presence of a softly-broken $\mathrm{Z}_2$ symmetry throughout the scalar and Yukawa sectors, as the additional gauge…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
Nucleic acid sensing is crucial for advancing diagnostics, therapeutic monitoring and molecu-lar biology research, by enabling the precise identification of DNA and RNA interactions. Here, we present an innovative sensing platform based on…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
Chemotaxis systems play a crucial role in modeling the dynamics of bacterial and cellular behaviors, including propagation, aggregation, and pattern formation, all under the influence of chemical signals. One notable characteristic of these…
We discuss theoretically the force F between two colloidal particles, each of them carrying one single strand DNA. The two strands are complementary only on a finite sequence of consecutive base pairs. We define an adjustment length (a few…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…