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Analysis of Correlations Between Sites in Models of Protein Sequences

Giraud, B. G.; Lapedes, Alan; Liu, Lon Chang - Santa Fe Institute - 1998

correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations … states at each site. Elementary models, where explicit results can be derived easily, are introduced. The number of states …

Persistent link: https://www.econbiz.de/10005790763

Lapedes, A. S.; Giraud, B. G.; Liu, L. C.; Stormo, G. D. - Santa Fe Institute - 1997

Covariation analysis of sets of aligned sequences for RNA molecules is relatively successful in elucidating RNA secondary structure, as well as some aspects of tertiary structure [Gutell(1992)]. Covariation analysis of sets of aligned sequences for protein molecules is successful in certain...

Persistent link: https://www.econbiz.de/10005790847

Applying Network Theory to Epidemics: Control Measures for Outbreaks of Mycoplasma pneumoniae

Ancel, Lauren W.; Newman, M. E. J.; Martin, Michael; … - Santa Fe Institute - 2001

Mycoplasma pneumoniae is a major cause of bacterial pneumonia in the United States. Outbreaks of illness due to mycoplasma commonly occur in closed or semi-closed communities. These outbreaks are difficult to contain due to delays in outbreak detection, the long incubation period of the...

Persistent link: https://www.econbiz.de/10005790696

Dynamics of a Simple Evolutionary Process

Stauffer, Dietrich; Newman, M. E. J. - Santa Fe Institute - 2001

-Sneppen model and models based on the so-called record dynamics. We confirm our analytic results with extensive numerical …

Persistent link: https://www.econbiz.de/10005260362

Classification of Long-Term Evolutionary Dynamics

Bedau, Mark A.; Snyder, Emile; Packard, Norman H. - Santa Fe Institute - 1998

We present empirical evidence that long-term evolutionary dynamics fall into three distinct classes, depending on whether adaptive evolutionary activity is absent (class 1), bounded (class 2), or unbounded (class 3). These classes are defined using three statistics: diversity, new evolutionary...

Persistent link: https://www.econbiz.de/10005837717

Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation

Wills, Peter R.; Kauffman, Stuart A.; B\"arbel M. R. Stadler - Santa Fe Institute - 1997

The theory of autocatalytic binary ligation is reviewed within the context of a rigorously applied Michaelis-Menten quasi-steady-state approximation to obtain explicit analytical results describing time-course data from experiments. A detailed protocol for the step-wise elucidation of a minimal...

Persistent link: https://www.econbiz.de/10005837730

Optimization in Complex Networks

Cancho, Ramon Ferrer i; Solé, Ricard V. - Santa Fe Institute - 2001

Many complex systems can be described in terms of networks of interacting units. Recent studies have shown that a wide class of both natural and artificial nets display a surprisingly widespread feature: the presence of highly heterogeneous distributions of links, providing an extraordinary...

Persistent link: https://www.econbiz.de/10005739984

The Role of Population Size, Pleiotropy, and Fitness Effects of Mutations in the Evolution of Overlapping Gene Functions

Wagner, Andreas - Santa Fe Institute - 2000

evolution of functional overlap and mean fitness are effectively decoupled, because they occur on different time scales. As a …

Persistent link: https://www.econbiz.de/10005740004

Error Propagation in the Hypercycle

Campos, P. R. A.; Fontanari, J. F.; Stadler, P. F. - Santa Fe Institute - 1999

We study analytically the steady-state regime of a network of n error-prone self-replicating templates forming an asymmetric hypercycle and its error tail. We show that the existence of a master template with a higher non-catalyzed self-replicative productivity, a, than the error tail ensures...

Persistent link: https://www.econbiz.de/10005623628

Developmental and Non-Developmental Morphospaces in Evolutionary Biology

Eble, Gunther J. - Santa Fe Institute - 1999

evolution, but any regularities encountered must reflect internal constraints and opportunities. Juvenile morphospaces are … likely to depict a range of pronounced allometries that can serve as raw material for evolution. I provide an extended … change in disparity through ontogeny. Still, all such developmental action potentially driving evolution occurs within a …

Persistent link: https://www.econbiz.de/10005623654