Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles

Article Abstract:

An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations of nucleic acids is reported. The corresponding algorithm 'concerted rotations with flexible bond angles' (CRA) for sampling polypeptides is found to be superior to local moves that included only flexible dihedral angles by allowing exploration of a larger conformational space as well as facilitating backbone transitions.

Usage, Chemical bonds, Monte Carlo method, Monte Carlo methods

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Size-expanded yDNA bases: An ab initio study

Article Abstract:

The structure and electronic properties of the y-bases are investigated. It is predicated that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result as it indicates that yDNA could have smaller HOMO-LUMO gap than the natural DNA.

Deoxyribonucleic Acid, DNA, Electron configuration, Structure, Atomic properties

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