Related papers: Melting behavior and different bound states in thr…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
We determine the three-body bound states of an atom in a Fermi mixture. Compared to the Efimov spectrum of three atoms in vacuum, we show that the Fermi seas deform the Efimov spectrum systematically. We demonstrate that this effect is more…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
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…