Fractals and hidden symmetries in DNA.
From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology
RNA viruses replicate as complex and dynamic mutant distributions. They are termed viral quasispecies, in recognition of the fundamental contribution of quasispecies theory in our understanding of error-prone replicative entities. Viral quasispecies have launched a fertile field of transdiciplinary research, both experimental and theoretical. Here we review the origin and some implications of the quasispecies concept, with emphasis on internal interactions...
Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
The Poisson-Boltzmann (PB) model is an effective approach for the electrostatics analysis of solvated biomolecules. The nonlinearity associated with the PB equation is critical when the underlying electrostatic potential is strong, but is extremely difficult to solve numerically. In this paper, we construct two operator splitting alternating direction implicit (ADI) schemes to efficiently and stably solve the nonlinear PB equation in a pseudo-transient continuation approach. The operator splitting...
Fuzzy Contact Maps Overlap for Protein Comparison: the Roles of Fitness and Normalization and the relation with Crisp Contact Maps.