We considered the propagation of nonlinear shallow water waves in a narrow channel presenting a fork. We aimed at computing the coupling conditions for a 1D effective model, using 2D simulations and an analysis based on the conservation laws. For small amplitudes, this analysis justifies the well-known Stoker interface conditions, so that the coupling does not depend on the angle of the fork. We also find this in the numerical solution. Large amplitude solutions in a symmetric fork also tend to follow Stoker’s relations, due to the symmetry constraint. For non symmetric forks, 2D effects dominate so that it is necessary to understand the flow inside the fork. However, even then, conservation laws give some insight in the dynamics.

New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology.