Related papers: Generalized Poland-Scheraga denaturation model and…
The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by…
A single model is presented which represents both of the two apparently unrelated localisation problems of the title. The phase diagram of this model is examined using scaling ideas and numerical simulations. It is argued that the…
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 Peierls-Nabarro (PN) model for dislocations is a hybrid model that incorporates the atomistic information of the dislocation core structure into the continuum theory. In this paper, we study the convergence from a full atomistic model…
A molecular dynamics simulation of the demixing process of a binary complex plasma is analysed and the role of distinct interaction potentials is discussed by using morphological Minkowski tensor analysis of the minority phase domain growth…
We revisit the popular notion of effective or renormalized charge, which is a concept of central importance in the field of highly charged colloidal or polyelectrolyte solutions. Working at the level of a linear Debye-H\"uckel like theory…
This paper studies the discretization of a homogenization and dimension reduction model for the elastic deformation of microstructured thin plates proposed by Hornung, Neukamm, and Vel\v{c}i\'c in 2014. Thereby, a nonlinear bending energy…
We consider a general model of a heterogeneous polymer chain fluctuating in the proximity of an interface between two selective solvents. The heterogeneous character of the model comes from the fact that the monomer units interact with the…
We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
For two-scale homogenization of a general class of asymptotically degenerating %uniformly strongly elliptic symmetric PDE systems with a critically scaled high contrast in periodic coefficients of a small period $\varepsilon$, we derive a…
The paper compares the statistical description of physical-metallurgical processes and ceramic-polycrystalline evolutions, termed the normal grain growth (NGG), as adopted to soft- and chemically-reactive grains, with a Smoluchowski's…
The situation of the metastable phase decay on the several types of heterogeneous centers is considered. The method to spread the monodisperse approximation on the situation of the strong unsymmetry is presented. The simple analytical…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
The aim of the paper is to introduce an alternative notion of two-scale convergence which gives a more natural modeling approach to the homogenization of partial differential equations with periodically oscillating coefficients: while…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We consider the Dyson hierarchical version of the quantum Spin-Glass with random Gaussian couplings characterized by the power-law decaying variance $\overline{J^2(r)} \propto r^{-2\sigma}$ and a uniform transverse field $h$. The ground…
We study Gibbs distributions of spins taking values in a general compact Polish space, interacting via a pair potential along the edges of a generalized random graph with a given asymptotic weight distribution $P$, obtained by annealing…
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…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
The particle-hole Density Matrix Renormalization Group (p-h DMRG) method is discussed as a possible new approach to large-scale nuclear shell-model calculations. Following a general description of the method, we apply it to a class of…