Complex systems can be successfully modeled in computer simulations. Due to the high computational cost of the numerical algorithms, different techniques are adapted to suit particular time- and length scales. Consequently, molecular reactions and conformational dynamics of molecules are most often not represented simultaneously, which is in contrast with complex molecular systems, where the motion and chemical reactivity of molecules are coupled. Here I present a technique that is a hybrid between stochastic dynamics and kinetics and that can represent both the spatio-temporal evolution and chemical reactivity in biological and chemical systems. Modeling of two classes of systems will be presented; (I) the spreading of epigenetic modifications on chromatin so as to model the establishment of gene expression patterns that account for phenotypic diversity of multicellular organisms, (II) the formation of informational sequences such as the DNA.