From a melt of rings to chromosome territories: the role of topological constraints in genome folding

JD Halverson, J Smrek, K Kremer… - Reports on Progress in …, 2014 - iopscience.iop.org
We review pro and contra of the hypothesis that generic polymer properties of topological
constraints are behind many aspects of chromatin folding in eukaryotic cells. For that …

Macrocyclic polymers: Synthesis, purification, properties and applications

J Ochs, CA Pagnacco, F Barroso-Bujans - Progress in Polymer Science, 2022 - Elsevier
Cyclic polymers present a topology that differ significantly from their linear counterparts due
to their circular structure and therefore, the lack of chain ends. These simple characteristics …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

Facile mechanochemical cycloreversion of polymer cross-linkers enhances tear resistance

S Wang, Y Hu, TB Kouznetsova, L Sapir, D Chen… - Science, 2023 - science.org
The mechanical properties of covalent polymer networks often arise from the permanent end-
linking or cross-linking of polymer strands, and molecular linkers that break more easily …

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

D Jost, P Carrivain, G Cavalli… - Nucleic acids research, 2014 - academic.oup.com
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states.
These domains are stably inherited across many cell generations and can be remodeled in …

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

DB Brückner, H Chen, L Barinov, B Zoller, T Gregor - Science, 2023 - science.org
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion of distal …

Kremer–Grest models for commodity polymer melts: Linking theory, experiment, and simulation at the Kuhn scale

R Everaers, HA Karimi-Varzaneh, F Fleck… - …, 2020 - ACS Publications
The Kremer–Grest (KG) polymer model is a standard model for studying generic polymer
properties in molecular dynamics simulations. It owes its popularity to its simplicity and …

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

JD Halverson, WB Lee, GS Grest… - The Journal of …, 2011 - pubs.aip.org
Molecular dynamics simulations were conducted to investigate the structural properties of
melts of nonconcatenated ring polymers and compared to melts of linear polymers. The …

Understanding and modeling polymers: The challenge of multiple scales

F Schmid - ACS Polymers Au, 2022 - ACS Publications
Polymer materials are multiscale systems by definition. Already the description of a single
macromolecule involves a multitude of scales, and cooperative processes in polymer …

Nonlinear shear rheology of entangled polymer rings

D Parisi, S Costanzo, Y Jeong, J Ahn, T Chang… - …, 2021 - ACS Publications
Steady-state shear viscosity η (γ̇) of unconcatenated ring polymer melts as a function of the
shear rate γ̇ is studied by a combination of experiments, simulations, and theory …