To explore this phenomenon, Zhang and Qi used a technique called molecular dynamics simulation, which can model how a molecular system changes over time. At the beginning of the simulation, the proteins and RNA that make up the nucleoli are randomly distributed throughout the nucleus, and the simulation tracks how they gradually form small droplets.
In their simulation, the researchers also included chromatin, the substance that makes up chromosomes and incudes proteins as well as DNA. Using data from previous experiments that analyzed the structure of chromosomes, the MIT team calculated the interaction energy of individual chromosomes, which allowed them to provide realistic representations of 3D genome structures.
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