Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
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 study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
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…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
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…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…
In this paper, we continue to study factorization of supersymmetric (SUSY) transformations in one-dimensional Quantum Mechanics into chains of elementary Darboux transformations with nonsingular coefficients. We define the class of…
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…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…
Quantum Mechanics SUper-SYmmetry (QM-SUSY) provides a general framework for studies using phenomenological potentials for nucleons (or clusters) interacting with a core. The SUSY potentials result from the transformation of the mean field…
Different ways to incorporate two-dimensional systems, which are not amenable to separation of variables, into the framework of Supersymmetrical Quantum Mechanics (SUSY QM) are analyzed. In particular, the direct generalization of…
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 present the general ideas on SuperSymmetric Quantum Mechanics (SUSY-QM) using different representations for the operators in question, which are defined by the corresponding bosonic Hamiltonian as part of SUSY Hamiltonian and its…
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…