The emergence of cooperation in Prisoner's Dilemma (PD) games is generally assumed to require repeated play (and strategies such as Tit-For-Tat, involving memory of previous interactions) or features ("tags") permitting cooperators and defectors to distinguish one another. In the Demographic...

The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are realized much more...

In the minds of the lay public, or even of scientists from unrelated fields, physics is mainly associated with extremes: big bangs and big bucks; the cosmic and the subnucleonic scales; matter in its most rarefied form such as single trapped atoms; or measurements of extraordinary precision to...

Shape space was proposed by Perelson and Oster 20 years ago as a conceptual formalism in which to represent antibody/antigen binding. It has since played a key role in computational immunology. Antigens and antibodies are thought of as points in an abstract "shape space" where coordinates of...

We study cellular automata where the state at each site is decided by a majority vote of the sites in its neighborhood. These are equivalent, for a restricted set of initial conditions, to non-zero probability transitions in single spin-flip dynamics of the Ising model at zero temperature. <p> We...</p>

Synthesis of random libraries of polynucleotide sequences has become a standard procedure of biotechnology; in combination with amplification methods such as the polymerase chain reaction (PCR) [1] this allows for selection experiments in which large pools of sequences are screened for a...

A number of evolutionary models based on the iterated Prisoner's Dilemma with noise are discussed. Different aspects of the evolutionary behaviour are illustrated (i) by varying the trickiness of the game (iterated game, mistakes, misunderstandings, choice of payoff matrix), (ii) by introducing...

Mapping sequences onto biopolymer structures is characterized by redundancy since the numbers of sequences exceed the numbers of structures. The degree of Redundancy depends on the notion of structure. Two classes of biopolymers, RNA molecules and proteins are considered in detail. A general...

We describe a simple framework for micro simulation of city traffic. A medium sized excerpt of Dallas was used to examine different levels of simulation fidelity of a cellular automaton method for the traffic flow simulation and simple intersection model. We point out problems arising with the...

Feynman has shown that a closed, locally interacting quantum system is capable of performing deterministic computation. Fro two finite-size versions of such a computer, the Schrodinger equations are solved analytically. The probability that the comptuer yields a final result upon measurement is...