  Comprehensive simulations of the entire biochemistry of cells have great
potential to help physicians treat disease and help engineers design biological
machines. But such simulations must model networks of millions of molecular
species and reactions.
  The Stochastic Simulation Algorithm (SSA) is widely used for simulating
biochemistry, especially systems with species populations small enough that
discreteness and stochasticity play important roles. However, existing serial
SSA methods are prohibitively slow for comprehensive networks, and existing
parallel SSA methods, which use periodic synchronization, sacrifice accuracy.
  To enable fast, accurate, and scalable simulations of biochemistry, we
present an exact parallel algorithm for SSA that partitions a biochemical
network into many SSA processes that simulate in parallel. Our parallel SSA
algorithm exactly coordinates the interactions among these SSA processes and
the species state they share by structuring the algorithm as a parallel
discrete event simulation (DES) application and using an optimistic parallel
DES simulator to synchronize the interactions. We anticipate that our method
will enable unprecedented biochemical simulations.
