DNA in nanochannels: theory and applications

K Frykholm, V Müller, KK Sriram… - Quarterly Reviews of …, 2022 - cambridge.org
Nanofluidic structures have over the last two decades emerged as a powerful platform for
detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a …

Probing protein–DNA interactions and compaction in nanochannels

R Riehn - Current Opinion in Structural Biology, 2024 - Elsevier
DNA confined to nanofluidic channels with a cross-section from tens to hundreds of nm wide
and hundreds of microns long stretches in an equilibrium process free of flow or end …

Conformation of a comb-like chain free in solution and confined in a nanochannel: from linear to bottlebrush structure

Z Tang, X Pan, H Zhou, L Li, M Ding - Macromolecules, 2022 - ACS Publications
We study the conformation of a comb-like polymer chain in dilute solution from being in a
free state to being confined in a nanochannel by using Brownian dynamics simulations. In …

Flow-induced translocation and conformational transition of polymer chains through nanochannels: Recent advances and future perspectives

M Ding, L Li - Macromolecules, 2021 - ACS Publications
How polymer chains with different architectures translocate through narrow nanochannels
with the channel size much smaller than the chain size in flow fields remains a fundamental …

Escape dynamics of active ring polymers in a cylindrical nanochannel

C Li, Q Chen, M Ding - Soft Matter, 2024 - pubs.rsc.org
We explore the escape dynamics of active ring polymers confined in a cylindrical
nanochannel using Brownian dynamics. Our simulation results show that the escape time …

Alpha‐synuclein modulates the physical properties of DNA

K Jiang, S Rocha, A Westling… - … A European Journal, 2018 - Wiley Online Library
Fundamental research on Parkinson's disease (PD) most often focuses on the ability of α‐
synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell …

Statistical properties of a slit-confined wormlike chain of finite length

Y Teng, NT Andersen, JZY Chen - Macromolecules, 2021 - ACS Publications
The wormlike-chain model is commonly used to describe the statistical properties of DNA
and liquid-crystal polymers. Following the Green's function approach, here we present the …

Behaviors of a polymer chain in channels: from Zimm to Rouse dynamics

Z Wang, ZG Wang, AC Shi, Y Lu, L An - Macromolecules, 2023 - ACS Publications
The effects of confinement and hydrodynamic interactions on single-chain diffusion
behaviors are studied by using a combination of molecular dynamics and multiparticle …

Self-avoiding wormlike chain confined in a cylindrical tube: scaling behavior

JZY Chen - Physical Review Letters, 2018 - APS
Within a confining tube section, the multithreads of a strongly confined, backfolding polymer
exert the excluded-volume repulsions on each other and produce physical properties that …

Piston compression of semiflexible ring polymers in channels

P Cifra, T Bleha - Macromolecular Theory and Simulations, 2021 - Wiley Online Library
Molecular simulations in nanochannels are used to explore the compression elasticity of
ring polymers of stiffness (persistence length) similar to DNA. By combination with the …