Related papers: Modeling the interaction of DNA with alternating f…
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the…
We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal…
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…
We address the question of the quantitative relationship between thermodynamic phase transitions and topological changes in the potential energy manifold analyzing two classes of one dimensional models, the Burkhardt solid-on-solid model…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
We investigate a simple model corresponding to particles driven in opposite directions and interacting via a repulsive potential. The particles move off-lattice on a periodic strip and are subject to random forces as well. We show that this…
Anisotropy of kinetic coefficients in presence of a magnetic field is represented by Hall currents, which appear in a collisional medium due to action of the Lorentz force on the charged particles between collisions. We derive equations,…
We investigate the spacetime properties of BTZ black holes in the presence of the Maxwell field and Born-Infeld field and find rich properties in the spacetime structures when the model parameters are varied. Employing the Landau-Lifshitz…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
I show that a model for the interaction of magnetic domains that includes a short range ferromagnetic and a long range dipolar anti-ferromagnetic interaction reproduces very well many characteristic features of two-dimensional magnetic…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
We analyse the effects of the environment (solvent quality, presence of extended structures - crowded environment) that may have impact on the order of the transition between denaturated and bounded DNA states and lead to changes in the…
We investigate the microscopic mechanism of the thermally induced ambient pressure ordered-disordered phase transitions of two zeolitic imidazolate frameworks of formula Zn(C$_3$H$_3$N$_2$)$_2$: a porous (ZIF-4) and a dense, non-porous…
We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble…