Selective advantage of topological disorder in biological evolution

We examine a model of biological evolution of Eigen's quasispecies in a holey fitness landscape, where the fitness of a site is either 0 (lethal site) or a uniform positive constant (viable site). So, the evolution dynamics is determined by the topology of the genome space. It is modeled by the random Bethe lattice. We use the effective medium and single-defect approximations to find the criteria, under which the localized quasispecies cloud is created. We find that shorter genomes, which are more robust to random mutations than average, represent a selective advantage which we call ``topological''. A way of assessing empirically the relative importance of reproductive success and topological advantage is suggested.Comment: 6 pages, 5 figures, svjour class, accepted in EPJ

Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.Comment: 45 pages, 20 figures, published, added Supplementary informatio