Stadler, P. F. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 463:7--19, 1999.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....replicating species, for example molecules, viroids, viruses, or bacteria. Fitness landscapes are understood as distributions of fitness values over sequence space and can be represented by mappings from sequence space into the real numbers, g : fI; d h ij g ) IR 1 (For recent reviews see [86, 93]) Herein the sequence space space is denoted by I and the distance between two sequences by d h ij . Several classes of model landscapes were either invented, like for example the Nk model [53] or adopted from physical models of spinglasses [99] in order to study replication and mutation with ....

Stadler, P. F., "Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers". J. Mol. Struct. (Theochem) 463 (1999):7--19. Peter Schuster 51

....replicating species, for example molecules, viroids, viruses, or bacteria. Fitness landscapes are understood as distributions of fitness values over sequence space and can be represented by mappings from sequence space into the real numbers, g : fI; d h ij g ) IR 1 (For recent reviews see [77, 83]) Herein the sequence space space is denoted by I and the distance between two sequences by d h ij . Several classes of model landscapes were either invented, like for example the Nk model [50] or adopted from physical models of spinglasses [89] in order to study replication and mutation with ....

Stadler, P. F., "Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers". J. Mol. Struct. (Theochem) 463 (1999):7--19.

....strong correlation between the fitness of a local optimum and the size of its basin of attraction [83, 84] Biologically relevant fitness landscape apparently are not of this type, however. Their correlation seem to be less pronounced [25] while on the other hand neutrality plays a crucial role [26, 85]. Neutrality, i.e. the existence of neighboring configurations with the same fitness, appears to be just a way of achieving a smooth landscape, though as we have seen in the case of the BBB neutrality depends intimately on how one defines a neighbor. Therefore it comes as a surprise, that ....

Stadler, P. F. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 463:7--19, 1999.

.... This is a consequence of the fact that all four landscapes can be understood (at least approximately in the case of the folding energies) as a composition of the genotype phenotype map (mapping the sequence onto its secondary structure) and a (close to linear) evaluation of the secondary structure [26]. As a consequence, all four landscapes mostly reflect the regularities of the underlying genotype phenotype map. For instance, the strong distinction between even and odd modes reflects the dominating e#ect of base pair stacking, which always involves an even number of nucleotide positions. ....

P. F. Stadler. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 463:7--19, 1999.

.... This is a consequence of the fact that all four landscapes can be understood (at least approximately in the case of the folding energies) as a composition of the genotype phenotype map (mapping the sequence onto its secondary structure) and a (close to linear) evaluation of the secondary structure [25]. As a consequence, all four landscapes mostly re ect the regularities of the underlying genotype phenotype map. For instance, the strong distinction between even and odd modes re ects the fact that base pair stacking, which always involves an even number of nucleotide Fast Fourier Transform for ....

P. F. Stadler. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 463:7-19, 1999. Santa Fe Institute Preprint 97-11-082.

....are influenced by even number of nucleotides depending on the location of the affected base pair within a stack. A recent comparison of amplitude spectra for different landscapes based on folding short RNA chains indicates that the amplitude spectra of the free energy landscapes are typical [137]. 3.2.3 Distance Correlation Functions Most early work on RNA landscapes, e.g. 42, 145] uses a different type of correlation measure based on the Hamming distance. In [136, 139] a more general version starting with a collection of relations on V is introduced. Let be a relation on V . Then we ....

P. F. Stadler. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 1998. in press, Sante Fe Institute Preprint 97-11-082.

....for common resources. Many simulation studies in this field use ad hoc substitutes for biological fitness landscapes such as spin glass Hamiltonians. It can be shown, however, that the properties of a fitness landscape are determined almost exclusively by its underlying sequence structure map [28]. In the case of the most important biopolymers the landscapes deviate significantly from simple disordered systems. 2. RNA Secondary Structures Meaningful notions of structure are of course context depend: successful descriptions of active sites of enzymes (or ribozymes) or specific binding ....

P. F. Stadler. Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. (THEOCHEM), 1997. submitted.

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