Related papers: DNA melting in poor solvent
The phase diagram of star polymer solutions in a good solvent is obtained over a wide range of densities and arm numbers by Monte Carlo simulations. The effective interaction between the stars is modeled by an ultrasoft pair potential which…
We investigate numerically the finite-temperature phase diagrams of the extended Bose-Hubbard model in a two-dimensional square lattice. In particular, we focus on the melting of supersolid phases of two different crystal orderings, stripe…
We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
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 the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
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…
In experiments the two-dimensional systems are realized mainly on solid substrates which introduce quenched disorder due to some inherent defects. The defects of substrates influence the melting scenario of the systems and have to be taken…
We study melting in a two-dimensional system of classical particles with Gaussian-core interactions in disordered environments. The pure system validates the conventional two-step melting with a hexatic phase intervening between the solid…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
We consider $S=1$ triangular lattice Heisenberg antiferromagnets with a strong single-ion anisotropy $D$ that dominates over the nearest-neighbour antiferromagnetic exchange $J$. In this limit of small $J/D$, we study low temperature ($T…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
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…
The random disorder can drastically change the melting scenario of two-dimensional systems and has to be taken into account in the interpretation of the experimental results. We present the results of the molecular dynamics simulations of…
We investigate the behaviour of dipolar bosons in two dimensions. We describe the large density crystalline limit analytically while we use quantum Monte-Carlo to study the melting toward the Bose-Einstein condensate. We find strong…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…