Epistasis can lead to fragmented neutral spaces and contingency in evolution.
Proc Biol Sci 279:1734 (2012) 1777-1783
Abstract:
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space--namely, that networks of genomes encoding the same phenotype may not be connected by single mutational moves. We use the folding of RNA sequences into secondary structures as a model genotype-phenotype map and explore the neutral spaces corresponding to networks of genotypes with the same phenotype. In most of these networks, we find that it is not possible to connect all genotypes to one another by single point mutations. Instead, a network for a phenotypic structure with n bonds typically fragments into at least 2(n) neutral components, often of similar size. While components of the same network generate the same phenotype, they show important variations in their properties, most strikingly in their evolvability and mutational robustness. This heterogeneity implies contingency in the evolutionary process.The effect of topology on the structure and free energy landscape of DNA kissing complexes
ArXiv 1203.3577 (2012)
Abstract:
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.Coarse-grained modeling of DNA and DNA nanotechnology
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 244 (2012)
Effect of Bending Rigidity on the Knotting of a Polymer under Tension
ACS MACRO LETTERS 1:11 (2012) 1352-1356
How Peclet number affects microstructure and transient cluster aggregation in sedimenting colloidal suspensions
JOURNAL OF CHEMICAL PHYSICS 136:6 (2012) ARTN 064517