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 …

Atomistic energetics and critical twinning stress prediction in face and body centered cubic metals: recent progress

P Chowdhury, H Sehitoglu - Journal of …, 2018 - asmedigitalcollection.asme.org
This paper recounts recent advances on the atomistic modeling of twinning in body-centered
cubic (bcc) and face-centered cubic (fcc) alloy. Specifically, we have reviewed:(i) the …

Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools

K Frykholm, LK Nyberg, F Westerlund - Integrative Biology, 2017 - academic.oup.com
DNA–protein interactions are at the core of the cellular machinery and single molecule
methods have revolutionized the possibilities to study, and our understanding of these …

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 …

One-parameter scaling theory for DNA extension in a nanochannel

E Werner, GK Cheong, D Gupta, KD Dorfman… - Physical review letters, 2017 - APS
Experiments measuring DNA extension in nanochannels are at odds with even the most
basic predictions of current scaling arguments for the conformations of confined semiflexible …

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 …

Backfolding of DNA confined in nanotubes: Flory theory versus the two-state cooperativity model

A Muralidhar, KD Dorfman - Macromolecules, 2016 - ACS Publications
We compare two theories for backfolding of semiflexible polymers, such as DNA, confined in
circular tubes of diameter of the order of the persistence length of the macromolecule. The …

Evaluation of blob theory for the diffusion of DNA in nanochannels

D Gupta, AB Bhandari, KD Dorfman - Macromolecules, 2018 - ACS Publications
We have measured the diffusivity of λ-DNA molecules in approximately square
nanochannels with effective sizes ranging from 117 to 260 nm at moderate ionic strength …

Measuring the wall depletion length of nanoconfined DNA

AB Bhandari, JG Reifenberger, HM Chuang… - The Journal of …, 2018 - pubs.aip.org
Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by
a lack of consensus regarding its wall depletion length. We have measured this quantity in …

Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis

J Krog, M Alizadehheidari, E Werner… - The Journal of …, 2018 - pubs.aip.org
Nanochannels provide a means for detailed experiments on the effect of confinement on
biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of …