HIV time hierarchy: Winning the war while, loosing all the battles
  AIDS is the pandemic of our era. A disease that scares us not only because it is fatal but also because its insidious time course makes us all potential carriers long before it hands us our heads in a basket. The strange three stage dynamics of aids is also one of the major puzzles in describing the disease theoretically (1). Aids starts, like most diseases, in a peak of virus expression (2,3), which is practically wiped out by the immune system. However it then remains in the body at a low level of expression until later (some time years later) when there is an outbreak of the disease which terminally cripples the immune system causing death from various common pathogens. In this paper we show, using a microscopic simulation, that the time course of AIDS is determined by the interactions of the virus and the immune cells in the shape space of antigens and that it is the virus's ability to move more rapidly in this space (it's high mutability) that causes the time course and eventual 'victory' of the disease. These results open the way for further experimental and therapeutic conclusions in the ongoing battle with the HIV epidemic. 
Uri Hershberg, Yoram Louzoun, Henri Atlan and Sorin Solomon