Understanding the relationship between genotype and phenotype is essential for understanding evolutionary dynamics. RNA is an extremely simple yet highly instructive case: both genotype (sequence) and phenotype (structure) are different aspects of a single molecule. The influence of the generic...

We have analyzed the interplay between noise and periodic modulations in a mean field model of a neural excitable medium. To this purpose, we have considered two types of modulations; namely, variations of the resistance and oscillations of the threshold. In both cases, stochastic resonance is...

This paper illustrates that artificial morphogenesis can be a computationally efficient technique. Artificial morphogenesis can develop graph grammar into modular Artificial Neural Networks (ANN), made of a combination of more simple sub-networks. The genetic algorithm is used to evolve coded...

We exhibit some simple gadgets useful in designing shallow parallel circuits for quantum algorithms. We prove that any quantum circuit composed entirely of controlled-not gates or of diagonal gates can be parallelized to logarithmic depth, while circuits composed of both cannot. Finally, while...

The fact that correlation does not imply causation is well known. correlation between variables at two sites does not imply that the two sites directly interact, because e.g., correlation between distant sites may be induced by chaining of correlation between a set of intervening, directly...

RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis and modularity not only can be precisely defined and statistically measured, but reveal simultaneous...

Social insects---ants, bees, termites and wasps---exhibit a collective problem-solving ability (Deneubourg and Goss, 1989; Bonabeau et al., 1997). In particular, several ant species are capable of selecting the shortest pathway, among a set of alternative pathways, from their nest to a food source...

The number of distinct functional classes of single-stranded RNAs (ssRNAs) and the number of sequences representing them are substantial and continue to increase. Organizing this data in an evolutionary context is essential, yet traditional comparative sequence analyses require that homologous...

The paper: (1) Gives a general argument why research on nonlinear science in general and chaos in particular is important in economics and finance. (2) Puts forth two definitions of stochastic nonlinearity (IID-Linearity and MDS-Linearity) for nonlinear time series analysis and argues for their...

We discuss the repton model of agarose gel electrophoresis of DNA. We review previous results, both analytic and numerical, present a new numerical algorithm for the efficient simulation of the model, and suggest a new approach to the model's analytic solutions.