We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering ...

RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning d-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A d-neighbor is a structure that differs from the input structure...

Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmar...

A survey of pairing properties of nucleonic matter is presented that includes the off-shell propagation associated with short-range and tensor correlations. For this purpose, the gap equation has been solved in its most general form employing the complete energy and momentum dependence of the normal self-energy contributions. The latter correlations include the self-consistent calculation of th...

We propose to use the recently predicted two-dimensional "weak-pairing" px + ipy superfluid state of fermionic cold atoms as a platform for topological quantum computation. In the core of a vortex, this state supports a zero-energy Majorana mode, which moves to finite energy in the corresponding topologically trivial "strong-pairing" state. By braiding vortices in the "weak-pairing" state, unit...

For the traditional low Tc superconductors, the superconducting condensation energy is proportional to the change in energy of the ionic lattice between the normal and superconducting state, providing a clear link between pairing and the electron–ion interaction. Here, for the t-J model, we discuss an analogous relationship between the superconducting condensation energy and the change in the e...

We discuss the pairing gap, a measure for nuclear pairing correlations, in chains of spherical, semi–magic nuclei in the framework of self–consistent nuclear mean–field models. The equations for the conventional BCS model and the approximate projection–before–variation Lipkin–Nogami method are formulated in terms of local density functionals for the effective interaction. We calculate the Lipki...

We study the correlation energy associated with the pair fluctuations in BCS theory. We use a schematic two-level pairing model and discuss the behavior of the correlation energy across shell closures, including the even-odd differences. It is shown that the random phase approximation (RPA) to the ground state energy reproduces the exact solutions quite well both in the normal fluid and in the ...