Browsing by Author "Paturej, J."
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Item Open Access Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization(Institute of Physics Publishing Ltd., 2023-07-26) Paturej, J.; Erbaş, AykutInterphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic chromatin loops present in interphase chromosomes, while the rigid core models the chromocenter section of the chromosome. Our simulations show that the colloidal chromosome model provides a well-separated particle distribution without specific attraction between the chain monomers. As the polymerization degree of the grafted cyclic chains decreases while maintaining the total chromosomal length (e.g. the more potent activity of condensin-family proteins), the average chromosomal volume becomes smaller, inter-chromosomal contacts decrease, and chromocenters organize in a quasi-crystalline order reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Notably, linear-polymer grafted particles also provide the same chromocenter organization scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. Our simulations show that polymer-grafted colloidal systems could help decipher 3D genome architecture along with the fractal globular and loop-extrusion models.Item Open Access Structural properties of cyclic polyelectrolytes in a dilute good solvent(American Chemical Society, 2023-12-25) Grzyb, A.; Haydukivska, K.; Klos, J. S.; Erbaş, Aykut; Paturej, J.Cyclic polymers display unique physical behaviors in comparison to those of their linear counterparts. Theoretical, computational, and experimental studies have revealed that some of their distinctive properties are also observed in charged variants of cyclic polymers, known as cyclic polyelectrolytes (PEs), especially in terms of their structural responses to variations in the strength of electrostatic interactions. In this study, we investigate the impact of cyclic topology on the conformations of PE chains in a dilute good solvent using scaling analysis and coarse-grained bead-spring molecular dynamics simulations. Our observations indicate that, in contrast to linear PE chains, cyclic topology results in more compact conformations at low and intermediate Bjerrum lengths. Moreover, two structural metrics, asphericity and prolateness, which quantify deviations from spherical and flat molecular shapes, exhibit nonmonotonic behaviors for cyclic PEs. This stands in contrast to linear PEs, where these shape characteristics exhibit a monotonic trend with an increasing Bjerrum length. A feasible analytical theory, developed to account for the ionic distributions around cyclic PE chains, suggests that the fundamental difference between the linear and cyclic chain conformations may be attributed to the topological effects influencing long-range electrostatic interactions.