Our topic is the segregation of ribosomes to the cytoplasmic periphery and the compaction of chromosomal DNA into a region of space called the nucleoid inside the E. coli cell. The goal of our research is to understand the driving forces behind this kind of spatial distribution. The picture of the nucleoid inferred from EM studies of thin slices of cryo-fixed E. coli is that of a multi-armed “octopus”. So we explore a highly simplified physical model of the cytoplasm where the plectonemic DNA is represented as a hyper-branched, freely-jointed polymer chain of hard spheres, while the ribosomes are represented as mobile hard spheres with smaller size. Based on current analyses, it is concluded that part of the driving forces comes from the excluded volume effect, the entropy effect and the structure of ribosomes.
