Combinatorial optimization problems defined on sets of phylogenetic trees are an important issue in computational biology, for instance the problem of reconstruction a phylogeny using maximum likelihood or parsimony approaches. The collection of possible phylogenetic trees is arranged as a...

We present a new style of molecular dynamics and self-assembly simulation, the Lattice Polymer Automaton (LPA). In the LPA all interactions, including electromagnetic forces, are decomposed and communicated via propagating particles, ``photons.'' The monomer-monomer bond forces, the molecular...

A measure of search difficulty, fitness distance correlation (FDC), is introduced and its power as a predictor of genetic algorithm (GA) performance is investigated. The sign and magnitude of this correlation can be used to predict the performance of a GA on many problems where the global maxima...

The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected graphs. A polynomial time algorithm for the computation of a minimum weight directed circuit basis is...

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...

We introduce an analytical model that predicts the dynamics of a simple evolutionary algorithm in terms of the flow in the space of fitness distributions. In the limit of infinite populations the equations of motion are derived in closed form. We show how finite populations induce periods of...

Explicit formulas for the metric and affine connections on the space of finite measures and probability measures are derived in different coordinate systems. They are transformed and compared with previous formulas of Cencov, Amari, and others. These formulas are given for finite sample spaces...

Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in standing diversity, correlations between rates of...

The study of social networks, and in particular the spread of disease on networks, has attracted considerable recent attention in the physical and mathematical literature. In this paper, we show that a large class of standard epidemiological models, the so-called susceptible/infective/recovered...