Cross-reactive memory responses occur when the immune system is primed by one strain of a pathogen and challenged with a related, but different strain. Much of the nature of a cross-reactive response is determined by the quantity and distribution of the memory cells, raised to the primary...

This paper describes a computer program, called Copycat, that models how people make analogies. It might seem odd to include such a topic in a collection of papers mostly on the immune system. However, the immune system is one of many systems in nature in which a very large collection of...

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...

We describe a method of implementing efficient computer simulations of immune systems that have a large number of unique B and/or T cell clones. The method uses an implementation technique called lazy evaluation to create the illusion that all clones are being simulated, while only actually...

During primary HIV infection the viral load in plasma increases, reaches a peak, and then declines. Phillips has suggested that the decline is due to a limitation in the number of cells susceptible to HIV infection, while other authors have suggested that the decline in viremia is due to an...

The immune system is a complex system that learns, remembers what it has learned, and acts to protect us from a variety of pathogens. Here we address the question of how the immune system is able to recognize and learn about pathogens that can rapidly evolve and hence potentially change so as to...