  Biological systems, unlike physical or chemical systems, are characterized by
the very inhomogeneous distribution of their components. The immune system, in
particular, is notable for self-organizing its structure. Classically, the
dynamics of natural systems have been described using differential equations.
But, differential equation models fail to account for the emergence of
large-scale inhomogeneities and for the influence of inhomogeneity on the
overall dynamics of biological systems. Here, we show that a microscopic
simulation methodology enables us to model the emergence of large-scale objects
and to extend the scope of mathematical modeling in biology. We take a simple
example from immunology and illustrate that the methods of classical
differential equations and microscopic simulation generate contradictory
results. Microscopic simulations generate a more faithful approximation of the
reality of the immune system.
