Related papers: Partly melted DNA conformations obtained with a pr…
Equilibrium phase diagrams for neutron star matter at subnuclear densities are obtained at zero temperature. Spherical, rod-like and slab-like nuclei as well as spherical and rod-like nuclear bubbles are taken into account by using a…
In two previous papers a semi-analytical model was presented for the hierarchical clustering of halos via gravitational instability from peaks in a random Gaussian field of density fluctuations. This model is better founded than the…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
We compute profile likelihoods for a stochastic model of diffusive transport motivated by experimental observations of heat conduction in layered skin tissues. This process is modelled as a random walk in a layered one-dimensional material,…
This contribution is devoted to cover some technical aspects related to the use of the recently proposed energy probability distribution zeros in the study of phase transitions. This method is based on the partial knowledge of the partition…
We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
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 describe an expert system, MAIES, developed for analysing forensic identification problems involving DNA mixture traces using quantitative peak area information. Peak area information is represented by conditional Gaussian distributions,…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
The method of Probability Density Profile Analysis has been introduced previously as a tool to find the best match between a set of experimentally generated Residual Dipolar Couplings and a set of known protein structures. While it proved…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
We investigate nuclear pasta structures at high temperatures in the framework of relativistic mean field model with Thomas-Fermi approximation. Typical pasta structures (droplet, rod, slab, tube, and bubble) are obtained, which form various…
We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…