Related papers: Coarse-grained modelling of supercoiled RNA
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
We have calculated the one-electron susceptibility of hydrated NaxCoO2 and find strong nesting nearly commensurate with a 2X2 superstructure. The nesting involves about 70% of all electrons at the Fermi level and is robust with respect to…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
A highly deformable rod, modelled as the extensible elastica, is connected to a movable clamp at one end and to a pin sliding along a frictionless curved profile at the other. Bifurcation analysis shows that axial compliance provides a…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Biological filaments such as DNA or bacterial flagella are typically curved in their natural states. To elucidate the interplay of viscous drag, twisting, and bending in the overdamped dynamics of such filaments, we compute the steady-state…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
To explore the role of the olivine grain size and crystal preferred orientation (CPO) on the evolution of the microstructure and the mechanical behaviour of upper mantle rocks up to large strains, we performed axial extension experiments at…