Related papers: Generalized Poland-Scheraga denaturation model and…
This paper is an extension of the result by Christowiak and Kreisbeck (2017), which addresses the Gamma-convergence approach to a homogenization problem for composite materials consisting of two distinct types of parallel layers. In…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
One dimensional pinning models have been widely studied in the physical and mathematical literature, also in presence of disorder. Roughly speaking, they undergo a transition between a delocalized phase and a localized one. In mathematical…
We consider general disordered models of pinning of directed polymers on a defect line. This class contains in particular the $(1+1)$--dimensional interface wetting model, the disordered Poland--Scheraga model of DNA denaturation and other…
We investigate the two-dimensional melting of deformable polymeric particles with multi-body interactions described by the Voronoi model. We report machine learning evidence for the existence of the intermediate hexatic phase in this…
We study a renormalizable four dimensional model with two deformed quantized space directions. A one-loop renormalization is performed explicitly. The Euclidean model is connected to the Minkowski version via an analytic continuation. At a…
We investigate a field theory for RNA-like polymers with periodic base sequence GCGCG..., where only single-strands aligned in the same direction form double strands. The field theory is derived from a lattice model that incorporates…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We consider disordered models of pinning of directed polymers on a defect line, including (1+1)-dimensional interface wetting models, disordered Poland--Scheraga models of DNA denaturation and other (1+d)-dimensional polymers in interaction…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
The resonance states and the decay dynamics of the nonlinear Schr\"odinger (or Gross-Pitaevskii) equation are studied for a simple, however flexible model system, the double delta-shell potential. This model allows analytical solutions and…
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…
A novel analysis of homogeneous nucleation of dislocations in sheared two-dimensional crystals described by periodized discrete elasticity models is presented. When the crystal is sheared beyond a critical strain $F=F_{c}$, the strained…
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…
In this work, we study the effective behavior of a two-dimensional variational model within finite crystal plasticity for high-contrast bilayered composites. Precisely, we consider materials arranged into periodically alternating thin…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…