During an immune response the affinity of antibodies that react with the antigen that triggered the response increases with time, a phenomenon known as affinity maturation. The molecular basis of affinity maturation has been partially elucidated. It involves the somatic mutation of immunoglobin...

We propose a new function for describing the rate of T cell proliferation in response to peptides on antigen presenting cells. The model improves an earlier model of ours by allowing for a true maximum proliferation rate of the T cells. This is achieved by a simple change of variables that...

We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by MasCaskill (1990). By analyzing the full distribution of base pair probabilities instead of a restricted number of secondary...

A binary model of the immune system is used to study the effects of evolution on the genetic encoding for antibody molecules. We report experiments which show that the evolution of immune system genes, simulated by the genetic algorithm, can induce a high degree of genetic organization even...

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...

In observational studies of HIV-1 pathogenesis to date, increased viral load has been shown to correlate with CD4 lymphocyte depletion and disease progression.$^{1-9}$ However, relatively little information is available on the kinetics of virus and CD4 lymphocyte turnover in vivo. In this...

We study the equilibrium binding properties of multivalent ligands to cell surface receptors. In contrast to most of the previous studies, which assumed the ligand concentration to be much larger than the receptor concentration, we examine the influence on the binding properties of cell density...

The binding of antibody to antigen or T-Cell receptor to major histocompatibility complex-peptide complex requires that portions of the two structures have complementary shapes that can closely approach each other. The question that we address here is how large should the complementary regions...

We extend an earlier model of protein evolution on a rugged landscape (Macken, C.A. & Perelson, A.S., {\it Proc. Natl. Acad. Sci. USA} {\bf 86,} 6191 (1989)) to the case in which the landscape exhibits a variable degree of correlation (i.e., smoothness). Correlation is introduced by assuming...

We develop a probability based model that suggests a novel explanation for the enormous diversity of the lymphocyte repertoire in the immune system. Taking into account the fraction of the repertoire that is expected to be rendered tolerant because of potential self reactivity, we calculate...