We report on the continuing research program at the Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here: (1) the use of coevolving adaptive neural networks for determining predictable protein structure classifications, and...

The repton model is a simple model of the ``reptation'' motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere interactions diffusing on a one-dimensional lattice....

In previous work, the speef of locally coupled quantum computers with infinite size clocks has been investigated in detail. One of the results is that the Feynman quantum computer and the Margolus cellular automaton compute at a constant rate. We show that this is no longer true for computers...

Using a new mathematical model to analyze a detailed set of viral load data collected from five infected patients after the administration of a potent inhibitor of HIV-1 protease, it was estimated that productively infected cells have, on average, a lifespan of 2.2 days (t[sub 1/2]=1.6 days) and...

A long history of dynamical analyses of food-web networks has led to important insights into the effects of complexity, omnivory and interaction strength on food-web stability. Some recent insights are based on nonlinear bioenergetic consumer-resource models that display chaotic behavior in...

Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as certain structural elements (sub-graphs). First order asymptotics are derived and their dependence on...

In this paper we describe the application of massively parallel processing (MPP) to the problems involve sequences of numbers (for example, the daily closing values of the stock market, EEG patterns of brainwave activity, or, as discussed in this paper, the temporal values from set of equations...

This paper presents an agent-based, object-oriented ecological model of forest dynamics designed to examine the role of disturbance on diversity. Arborscapes is based on Swarm, an agent-based software platform that offers advantages for ecological modeling, including a suite of standardized...