Related papers: Generalized Poland-Scheraga denaturation model and…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The Transfer-Integral (TI) operator is a powerful method to investigate the statistical physics of 1-dimensional models, like those used to describe DNA denaturation. At the cost of a certain number of approximations, the TI equation can be…
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.…
The rise of machine learning in image processing has created a gap between trainable data-driven and classical model-driven approaches: While learning-based models often show superior performance, classical ones are often more transparent.…
The two-scale computational homogenization method is proposed for modelling of locally periodic fluid-saturated media subjected a to large deformation induced by quasistatic loading. The periodic heterogeneities are relevant to the…
We present a three dimensional, time dependent model for bone regeneration in the presence of porous scaffolds to bridge critical size bone defects. Our approach uses homogenized quantities, thus drastically reducing computational cost…
For a general renewal process $N$ (allowing delay, defect and multiple simultaneous arrivals) the independence of the first renewal epochs of the marked processes got from $N$ by Bernoulli $0$/$1$ thinning is characterized. This…
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…
We present and establish large deviations principles for general multivariate renewal-reward processes associated with a classical discrete-time renewal process. A renewal-reward process describes a cumulative reward over time, supposing…
Real crystals almost unavoidably contain a finite density of dislocations. We show that this generic type of long--range correlated disorder leads to a breakdown of the conventional scenario of critical behavior and standard renormalization…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
The vertex model with homogeneous cell properties is known to exhibit a parameter degeneracy in which the system's dynamics is independent of the target area. Here, we show, for the heterogeneous vertex model where cells differ in size and…
We demonstrate that the source of a shear-free null congruence is, generically, a world sheet of a singular string in the complex Minkowski space. In particular cases the string degenerates into the Newman's point singularity. We describe…
Identifying disease-indicative genes is critical for deciphering disease mechanisms and has attracted significant interest in biomedical research. Spatial transcriptomics offers unprecedented insights for the detection of disease-specific…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
The starting point for this work is a static macroscopic model for a high-contrast layered material in single-slip finite crystal plasticity, identified in [Christowiak & Kreisbeck, Calc. Var. PDE (2017)] as a homogenization limit via…
A dynamical study of the decay of a metastable state by quantum tunneling through an anisotropic, non separable, two-dimensional potential barrier is performed by the numerical solution of the time-dependent Schrodinger equation. Initial…