Abstract: Methods of determining a therapy for inhibiting growth or pathogenesis of one or more cell colonies based on modeling intracellular and/or intercellular communication mechanisms utilized by the cell type(s) in question, selective pressures on the one or more cell colonies within a cell population, and therapies or therapeutic agents available to a user. A dynamic molecular-level model of a cell population representing one or more cell colonies models differing aspects of one or more resistance forming mechanisms and the effects that the available treatment agents or therapies may have on the differing aspects. The dynamic molecular-model, in combination with a selective pressure model, formulates an optimization problem that is solved to determine amounts of the differing treatment agents or therapies.