Long chain molecules can be entropically compacted in a crowded medium. We study the compaction transition of a heterogeneous polymer with ring topology by crowding effects in a free or confined space. For this, we use molecular dynamics simulations in which the effects of crowders are taken into account through effective interactions between chain segments. Our parameter choices are inspired by the Escherichia coli chromosome. The polymer consists of small and big monomers; the big monomers dispersed along the backbone are to mimic the binding of RNA polymerases. Our results show that the compaction transition is a two-step process: initial compaction induced by the association (clustering) of big monomers followed by a gradual overall compaction. They also indicate that cylindrical confinement makes the initial transition more effective; for representative parameter choices, the initial compaction accounts for about 60% reduction in the chain size. Our simulation results support the view that crowding promotes clustering of active transcription units into transcription factories.
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7 August 2021
Research Article|
August 03 2021
Collapse transition of a heterogeneous polymer in a crowded medium
Special Collection:
Depletion Forces and Asakura-Oosawa Theory
Youngkyun Jung;
Youngkyun Jung
a)
1
Supercomputing Center, Korea Institute of Science and Technology Information
, Daejeon 34141, South Korea
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Bae-Yeun Ha
Bae-Yeun Ha
b)
2
Department of Physics and Astronomy, University of Waterloo
, Waterloo, Ontario N2L 3G1, Canada
b)Author to whom correspondence should be addressed: byha@uwaterloo.ca
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b)Author to whom correspondence should be addressed: byha@uwaterloo.ca
Note: This paper is part of the JCP Special Topic on Depletion Forces and Asakura-Oosawa Theory.
J. Chem. Phys. 155, 054902 (2021)
Article history
Received:
May 10 2021
Accepted:
July 13 2021
Citation
Youngkyun Jung, Bae-Yeun Ha; Collapse transition of a heterogeneous polymer in a crowded medium. J. Chem. Phys. 7 August 2021; 155 (5): 054902. https://doi.org/10.1063/5.0056446
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