Polymers under confinement: single polymers, how they interact, and as model chromosomes

BY Ha, Y Jung - Soft Matter, 2015 - pubs.rsc.org
How confinement or a physical constraint modifies polymer chains is not only a classical
problem in polymer physics but also relevant in a variety of contexts such as single-molecule …

Through the eye of the needle: recent advances in understanding biopolymer translocation

D Panja, GT Barkema… - Journal of Physics …, 2013 - iopscience.iop.org
In recent years polymer translocation, ie, transport of polymeric molecules through
nanometer-sized pores and channels embedded in membranes, has witnessed strong …

Sucking genes into pores: Insight into driven translocation

T Sakaue - Physical Review E—Statistical, Nonlinear, and Soft …, 2010 - APS
Flexible polymers such as long DNA, RNA molecules, and proteins, can pass through a
narrow pore whose size is comparable to their molecular thickness. We highlight the …

Extension of DNA in a nanochannel as a rod-to-coil transition

DR Tree, Y Wang, KD Dorfman - Physical review letters, 2013 - APS
DNA confinement in nanochannels is emerging as an important tool for genomics and an
excellent platform for testing the theories of confined wormlike polymers. Using cutting-edge …

Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories

AK Yesbolatova, R Arai, T Sakaue, A Kimura - Physical Review Letters, 2022 - APS
During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin
motion markedly decreases. Despite its biological implications, the underlying mechanism …

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

ZT Berndsen, N Keller, S Grimes… - Proceedings of the …, 2014 - National Acad Sciences
Many viruses use molecular motors that generate large forces to package DNA to near-
crystalline densities inside preformed viral proheads. Besides being a key step in viral …

Polymer looping is controlled by macromolecular crowding, spatial confinement, and chain stiffness

J Shin, AG Cherstvy, R Metzler - ACS Macro Letters, 2015 - ACS Publications
We study by extensive computer simulations the looping characteristics of linear polymers
with varying persistence length inside a spherical cavity in the presence of macromolecular …

Semiflexible polymers in spherical confinement: Bipolar orientational order versus tennis ball states

A Nikoubashman, DA Vega, K Binder, A Milchev - Physical review letters, 2017 - APS
Densely packed semiflexible polymers with contour length L confined in spheres with radius
R of the same order as L cannot exhibit uniform nematic order. Depending on the chain …

Directed self-organization of single DNA molecules in a nanoslit via embedded nanopit arrays

W Reisner, NB Larsen, H Flyvbjerg… - Proceedings of the …, 2009 - National Acad Sciences
We show that arrays of nanopit structures etched in a nanoslit can control the positioning
and conformation of single DNA molecules in nanofluidic devices. By adjusting the spacing …

Myoglobin unfolding in crowding and confinement

A Malik, J Kundu, SK Mukherjee… - The Journal of Physical …, 2012 - ACS Publications
Crowding and confinement have often been used synonymously with regard to their effect
on the structure and dynamics of proteins. In this work, we have investigated the unfolding of …