Related papers: Numerical study on a disordered model for DNA dena…
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.…
We study the 3d effective field theory of a weakly coupled two Higgs-doublet scalar model at high temperature. Our model has three scalar quartic couplings and an $O(4)$ symmetry which is spontaneously broken by a nonzero scalar field $vev$…
We consider a renewal process \tau={\tau_0,\tau_1,...} on the integers, where the law of \tau_i-\tau_{i-1} has a power-like tail P(\tau_i-\tau_{i-1}=n)=n^{-(\alpha+1)}L(n) with \alpha\ge0 and L(.) slowly varying. We then assign a random,…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…
We study the structural transition from `B' form of DNA to 'A' form of DNA using group theoretic methods. The transition is not of the order-disorder type and hence to construct a Landau kind of theory for the transition we define a higher…
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 discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
We study a 1D system with a power-law quasiparticle dispersion $\propto |k|^\alpha\sign k$ in the presence of a short-range-correlated random potential and demonstrate that for $\alpha<1/2$ it exhibits a disorder-driven quantum phase…
This study investigates the first-order phase transition within neutron stars, leveraging the deep neural network (DNN) framework alongside contemporary astronomical measurements. The equation of state (EOS) for neutron stars is delineated…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
The classification of structural phase transitions as displacive or order-disorder in character is usually based on spectroscopic data above the transition. We use single crystal x-ray diffraction to investigate structural correlations in…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
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 Ma-Dasgupta real-space renormalization methods allow to study disordered systems which are governed by strong disorder fixed points. After a general introduction to the qualitative ideas and to the quantitative renormalization rules, we…