We cast some classes of fitness landscapes as problems in spectral analysis on various Cayley graphs. In particular, landscapes derived from RNA folding are realized on Hamming graphs and analyzed in terms of Walsh transforms; assignment problems are interpreted as functions on the symmetric...

We report numerical simulations on the number of local minima in the landscape of the Graph Bipartitioning Problem and provide an

Mutation is introduced into autocatalytic reaction networks. The differential equations obtained are neither of replicator type nor can they be transformed straightway into a linear equation. Examples of low dimensional dynamical systems---$n= 2, 3 $, and 4---are discussed and complete...

The mean number (N) of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination numbers. For lattices with small connectivities, numerical simulations do not show any significant...

Shapes of biological macromolecules---RNA, DNA, and proteins---can be represented by abstract algebraic structures provided as suitably coarse resolution is chosen. These abstract structures, for instance partially ordered sets and permutation groups, can be used for deriving new metric...

According to the Darwinian theory of evolution, adaptation results from spontaneously generated genetic variation and natural selection. Mathematical models of this process can be seen as describing a dynamics on an algebraic structure which in turn is defined by the processes which generate...

Combinatorial optimization problems defined on sets of phylogenetic trees are an important issue in computational biology, for instance the problem of reconstruction a phylogeny using maximum likelihood or parsimony approaches. The collection of possible phylogenetic trees is arranged as a...

The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected graphs. A polynomial time algorithm for the computation of a minimum weight directed circuit basis is...

We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by MasCaskill (1990). By analyzing the full distribution of base pair probabilities instead of a restricted number of secondary...

Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of robustness would require a rethinking of key concepts in the field of molecular evolution, such...