Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying configuration space. The amplitude spectrum obtained from the Fourier transform contains information about the ruggedness of the landscape. It can be...

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...

Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more than 4000 nucleotides) infeasible on present-day workstations. An implementation of the...

Background: Protein space is explored by means of an inverse folding procedure that makes use of knowledge-based potentials of mean force. <p> Results: Computer simulations indicate that amino acid sequences folding into a common shape are distributed homogeneously forming extended percolating...</p>

The interplay of ruggedness and neutrality in fitness landscapes plays an important role in explaining the dynamics of evolutionary adaptation. While various measures of ruggedness (correlation functions, adaptive walks, or the density of local optima) are reasonably well understood, and models...

Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequence-structure relations in protein space. In particular, we test the following two propositions which were found to be...

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...

Correlation functions are important characteristics of (fitness) landscapes. We use the fourier expansion of landscapes in order to characterize the set of all the possible autocorrelation functions on highly symmetric graphs, as well as the isotropic random fields on such graphs. A canonical...

A class of autocatalytic reaction networks based on template dependent replication and specific catalysis is considered. Trimolecular "elementary strps" of simple replicator dynamics are resolved into two consecutive irreversible reactions. The extreme cases, competition for common resources and...

The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped with a notion of distance, for example, a Euclidean vector space. Recent computational work on a biophysical...