A Computational Model of Degeneracy in a Lymph Node - Artificial Immune Systems - page 168

cells populations in close proximity to the appropriate APCs and also apart from
each other until they are in a state in which they are ready to interact with each
other [13].

3.1 T H Activation in a Lymph Node
Naive T H cells become activated by APCs presenting MHC-II to which antigenic
peptides are bound (MHC-P). In order for this activation to take place, a certain
level of stimulation is required, an issue determined by two concepts known as
anity and avidity. Anity is simply the strength of binding between a single
binding site (e.g. T cell receptor) and a single ligand (e.g. an MHC-P complex).
It can be quantitatively measured using a dissociation constant K d ,whichisthe
concentration of a molecule X required to occupy half of the combining sites
of another molecule Y present in a solution. Hence, a smaller K d represents a
stronger or higher anity [13]. Anity differs from avidity, which is a measure
of the strength of binding between molecules or cells when there is more than
one binding site present [15].
T cells become activated when the concentration of MHC-P complexes on an
APC reaches a sucient threshold level [16]. In other words, T cells become
activatedwhenanaviditythresholdismet, and so T cell activation is affected
by both the anity between the T cell receptor and antigenic peptides presented
by the APC, and the concentration of these ligands present. It is possible, there-
fore, for an APC presenting high concentration of MHC-P complexes with weak
anity to activate a T cell, and conversely an APC presenting a low concen-
tration of MHC-P complexes with high anity not to activate a T cell. Once a
naive T cell has become activated it initiates a process of cellular proliferation
and differentiation into effector T cells that can perform their allotted immune
functions. In the case of effector T H cells, they play a crucial role in activating
both B and T C cells which are then in turn able to neutralise pathogens.

4 Degenerate Receptor Lymph Node Model

The previous section described how the activation of naive T H cells in the para-
cortex of the lymph node provides the initial recognition event of the adaptive
immune response to lymph-borne antigen. The computational model that is de-
scribed in this section aims to understand how this recognition event is affected
by notion that the antigen receptors of T H cells are degenerate. Specifically, the
model is an abstract representation of the activation of T H cells in the paracor-
tex of the lymph node based on the biological detail presented in section 3, and
the assumption that the T H cell receptors can bind to more than one antigen
epitope.

4.1 Overview

The first step in building the model was to extract the relevant details from
the biology to enable the identification of a suitable model type. The process