  Molecular ecology uses molecular genetic data to answer traditional
ecological questions in biogeography and biodiversity among others. Several
ecological principles, such as the niche hypothesis and the competitive
exclusions, are based on the fact that species compete for resources. More in
general, it is now recognized that species interactions play a crucial role in
determining the coexistence and abundance of species. However, experimentally
controllable platforms, which allow to study and measure competitions among
species, are rare and difficult to implement. In this work, we suggest to
exploit a Molecular Dynamics coarse-grained model to study interactions among
single strands of DNA, representing individuals of different species, which
compete for binding to other oligomers considered as resources. In particular,
the well-established knowledge of DNA-DNA interactions at the nanoscale allows
us to test the hypothesis that the maximum consecutive overlap between pairs of
oligomers measure the species competitive advantages. However, we suggest that
more complex structure also plays a role in the ability of the species to
successfully bind to the target resource oligomer. We complement the
simulations with experiments on populations of DNA strands which qualitatively
confirm our hypotheses. These tools constitute a promising starting point for
further developments concerning the study of controlled, DNA-based, artificial
ecosystems.
