Chemical Organization Theory Applied to Virus Dynamics

Chemical organization theory has been proposed to provide a new perspective to study complex dynamical reaction networks. It decomposes a reaction network into overlapping sub-networks called organizations. An organization is an algebraically closed and self-maintaining set of molecular species. The set of organizations form a hierarchical organizational structure, which is here a lattice. In order to evaluate the usefulness of this approach we apply the theory to five models of immune response to HIV infection. We found four different lattices of organizations, which can be used as a first classification of the models. Furthermore, each organization found can be assigned to a functional state of the system. And finally, the lattice of organizations can be used to explain a treatment strategy on a more abstract level, i.e., as a movement from one organization into another.