A minimal G$\bar{\textrm{o}}$-model for rebuilding whole genome structures from haploid single-cell Hi-C data

We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structure-based harmonic potential. We suggest and test two minimization protocols which consistently fold into conformationally similar low energy states. The latter are similar to previously published structures but are calculated in a fraction of the time. We find evidence that mere fulfillment of conta…