RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA ...

The accuracy of the Hartree-Fock method with an empirical dispersion correction, HF-D3, to model interaction energies and locate constrained minimum geometries is tested against more conventional correlation methods, such as second-order perturbation theory and coupled cluster theory, and against the sophisticated effective fragment potential model. HF-D3 was applied to substituted-benzene dime...

There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows r...

We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of ...

Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation...

Fluorescence energy transfer to graphene oxide is studied using covalently linked DNA probes ranging from 4 to 70 base pairs. The characteristic distance and mechanism of energy transfer are reported.

Pseudoknots are an essential feature of RNA tertiary structures. Simple H-type pseudoknots have been studied extensively in terms of biological functions, computational prediction, and energy models. Intramolecular kissing hairpins are a more complex and biologically important type of pseudoknot in which two hairpin loops form base pairs. They are hard to predict using free energy minimization ...

We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model. Persistence lengths calculated directly from th...

A typical form of mass formula is re-explained in terms of nuclear structure. For N ≈ Z nuclei, we propose to start with the shell model picture and to consider the T = 0 2n−2p (αlike) correlations as the fundamental concept, instead of the symmetry energy. Subsequently, the symmetry energy is described on the basis of the α-like superfluidity caused by the T = 0 2n− 2p correlations, in paralle...

A mean-field plus pairing model for atomic nuclei in the Fe region was studied using a finite-temperature quantum Monte-Carlo method. We present results for thermodynamical quantities such as the internal energy and the specific heat. These results give indications of a phase transition related to the pairing amongst nucleons, around temperatures of 0.7 MeV. The influence of the residual intera...