1. A computer system for recommending an optimal treatment protocol for a human patient comprising: a model of biological processes related to a disease for the human patient; a treatment protocol generator for generating a plurality of treatment protocols for treating the disease in the human patient using drugs; a treatment protocol generator that creates treatment protocol space; a selector adapted to select an optimal treatment protocol from said plurality of treatment protocols generated from the treatment protocol generator based on the model, and a computer processor; the model, further comprising: a pharmacokinetics macro module adapted to analyze interactions between a ligand and a population of target cells at a tissue level in the human patient; a pharmacokinetics micro module adapted to analyze interactions between the ligand and a cell at an individual cell level in the human patient; the micro module adapted to model behavior of the ligand and receptors related to single cell level of ligand-cell interactions, as a stochastic process; wherein the computer system outputs a recommendation for the optimal treatment protocol for the human patient to a user; and wherein the number of receptors is not constant.