  We present a probabilistic T-cell model that includes negative selection and
takes contrasting models of tissue-restricted antigen (TRA) expression in the
thymus into account. We start from the basic model of van den Berg, Rand, and
Burroughs (2001) and include negative selection via individual-based T-cell
modelling, in which each T-cell is defined by its stimulation rates to all
relevant self antigens. We present a simulation approach based on partial
tilting of the stimulation rates recognized by a single T-cell. We investigate
the effects of negative selection for diverging modes of thymic antigen
presentation, namely arbitrary TRA presentation, and more or less strict
emulation of tissue-specific cell lines. We observe that negative selection
leads to truncation of the tail of the distribution of the stimulation rates
mature T-cells receive from self antigens, i.e., the self background is
reduced. This increases the activation probabilities of single T-cells in the
presence of non-self antigens.
