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...

Computer codes for computation and comparison of RNA secondary structures, the {\tt Vienna RNA package}, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition...

Algorithms predicting RNA secondary structures based on different folding criteria---minimum free energy (mfe), kinetic folding (kin), maximum matching (mm)---and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter...

To distinguish continuous from discontinuous evolutionary change, a relation of nearness between phenotypes is needed. Such a relation is based on the probability of one phenotype being accessible from another through changes in the genotype. This is exemplified by calculating the shape...

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the vicinity of the minimum free energy. This enables the efficient approximation of statistical...

Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely defined base pairing pattern to every sequence. This mapping is non-invertible since many sequences fold into the same (secondary) structure or shape. The preimages of the map, called neutral networks,...

The evolution of RNA molecules in replication assays, viroids and RNA viruses can be viewed as an adaptation process on a ``fitness'' landscape. The dynamics of evolution is hence tightly linked to the structure of the underlying landscape. Global features of landscapes can be described by...

Evolution has created the complexity of the animate world and deciphering the language of evolution is the key toward understanding nature. The dynamics of evolution is simplified by considering it as a superposition of three less sophisticated processes: population dynamics, population support...

Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness among phenotypes, independently of their similarity. Because of neutrality, phenotypes denote...

Some global dynamical properties of catalytic networks, in particular permanence, are closely related with a directed graph representing the differential equation. It can be shown that for every directed graph with a Hamiltonian circuit there is a choice of rate constants such that the system is...