Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.polymer physics | Brownian dynamics | chromatin looping | nucleosome D NA in living cells associates with proteins that continuously bind and dissociate. Some proteins affect local structure (such as histones and histone-like proteins), whereas others act globally to compact whole chromosomal segments [such as CCCTC-binding factor (CTCF)] (1-3). Bound proteins also cluster into supramolecular structures; for example, different transcription factors often bind to the same hot spots in the fly genome (4), and active molecules of RNA polymerase II coassociate in transcription factories (5, 6). In the latter case, clustering generates high local concentrations that facilitate production of the appropriate transcripts, as well as organizing the genome in 3D space.Against this background, biophysicists have begun to model DNA folding driven by DNA-binding proteins (3,(7)(8)(9)(10)(11)(12). Usually, the effects of DNA binding are incorporated into an effective potential that influences DNA dynamics; for instance, by stipulating that selected protein-binding regions in the polymer attract each other (11,12). Here, we use molecular dynamics (MD) to model proteins that diffuse to DNA, bind, and dissociate. In the absence of any explicit mutual attraction between proteins or between monomers in the polymer, we uncover an emergent property of the system: binding spontaneously induces protein clustering and genome compaction. For example, simulations yield structures seen experimentally when proteins representing bacterial histone-like nucleoid-structuring protein (H-NS) (1, 2, 13), gold nanoparticles (14, 15), and nucleosome cores bind to DNA. Using data derived from ChIP coupled to high-throughput sequencing (ChIP-seq) (16), we also model binding of RNA polymerase II and its transcription factor, NFκB, to the appropriate (cognate) sites on four human chromosomes; the two proteins spontaneously cluster into factories that are surrounded by loops that reflect those detected in cells using chromatin inte...