ArticleBiophysical journal2015
Simulating the entropic collapse of coarse-grained chromosomes.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Depletion forces from interacting crowders.Physical review. E · 2026Article
- Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness.Soft matter · 2026Article
- Abundant positively-charged proteins underlie JCVI-Syn3A's expanded nucleoid and ribosome distribution.PLoS computational biology · 2026Article
- Review
- Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness.bioRxiv : the preprint server for biology · 2025Article
- Review
- Differentiating the roles of proteins and polysomes in nucleoid size homeostasis in Escherichia coli.Biophysical journal · 2024Article
- Article
- Machine learning classification of trajectories from molecular dynamics simulations of chromosome segregation.PloS one · 2022Article
- Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement.Entropy (Basel, Switzerland) · 2021Article
- Article
- The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid.Molecular microbiology · 2020Article
- Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans.Nature communications · 2019Article
- Formation of Chromatin Subcompartments by Phase Separation.Biophysical journal · 2018Review
- Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin.Scientific reports · 2018Article
- Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.The Journal of chemical physics · 2018Article
- Interfering With DNA Decondensation as a Strategy Against Mycobacteria.Frontiers in microbiology · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- A ring-polymer model shows how macromolecular crowding controls chromosome-arm organization in Escherichia coli.Scientific reports · 2017Article
- Chromosome, cell cycle, and entropy.Biophysical journal · 2015Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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