title: Simulating the entropic collapse of coarse-grained chromosomes.
abstract: Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.
authors.affiliation: The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, Theoretical Physics, University of Oxford, Oxford, United Kingdom. Electronic address: tyler.shendruk@physics.ox.ac.uk.
authors.forename: Tyler N
authors.initials: TN
authors.lastname: Shendruk
authors.affiliation: Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Bertrand
authors.affiliation: Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada.
authors.forename: Hendrick W
authors.initials: HW
authors.lastname: de Haan
authors.affiliation: Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
authors.forename: James L
authors.initials: JL
authors.lastname: Harden
authors.affiliation: Department of Physics, University of Ottawa, Ottawa, Ontario, Canada. Electronic address: gslater@uottawa.ca.
authors.forename: Gary W
authors.initials: GW
authors.lastname: Slater
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000737:chemistry*; D056004:Molecular Dynamics Simulation