The experimental evidence has clearly illustrated the fundamental difference between cytoplasmic and test tube.  It has also showed that the classical reaction kinetics approaches, such as the law of mass action, breakdown in in vivo conditions. As a consequence the attention of theoretical biochemists has focused in discovering the rate laws controlling reactions in vivo.  In recent years, theoreticians have been using computational frameworks to extract rate laws or empirical equations of reactions from direct numerical simulations.  In this talk we will discuss some of the simulation techniques which we have been using to explore reactions in in vivo conditions.  We will pay special attention is paid to the strengths and limitations of these modeling techniques and appropriate conditions under which each can be used.