Multi-scale coding of genomic information: From DNA sequence to genome structure and function

A Arneodo, C Vaillant, B Audit, F Argoul… - Physics Reports, 2011 - Elsevier
Understanding how chromatin is spatially and dynamically organized in the nucleus of
eukaryotic cells and how this affects genome functions is one of the main challenges of cell …

FiberApp: an open-source software for tracking and analyzing polymers, filaments, biomacromolecules, and fibrous objects

I Usov, R Mezzenga - Macromolecules, 2015 - ACS Publications
Biological semiflexible polymers and filaments such as collagen, fibronectin, actin,
microtubules, coiled-coil proteins, DNA, siRNA, amyloid fibrils, etc., are ubiquitous in nature …

Environment‐dependent stability and mechanical properties of DNA origami six‐helix bundles with different crossover spacings

Y Xin, P Piskunen, A Suma, C Li, H Ijäs, S Ojasalo… - Small, 2022 - Wiley Online Library
The internal design of DNA nanostructures defines how they behave in different
environmental conditions, such as endonuclease‐rich or low‐Mg2+ solutions. Notably, the …

Estimation of persistence lengths of semiflexible polymers: Insight from simulations

HP Hsu, W Paul, K Binder - Polymer Science Series C, 2013 - Springer
The persistence length of macromolecules is one of their basic characteristics, describing
their intrinsic local stiffness. However, it is difficult to extract this length from physical …

Breakdown of the Kratky-Porod wormlike chain model for semiflexible polymers in two dimensions

HP Hsu, W Paul, K Binder - Europhysics Letters, 2011 - iopscience.iop.org
Abstract By large-scale Monte Carlo simulations of semiflexible polymers in d= 2 dimensions
the applicability of the Kratky-Porod model is tested. This model is widely used as" standard …

How does stiffness of polymer chains affect their adsorption transition?

A Milchev, K Binder - The Journal of chemical physics, 2020 - pubs.aip.org
The adsorption transition and the structure of semiflexible adsorbed macromolecules are
studied by a molecular dynamics simulation of a coarse-grained, bead-spring type model …

Conformations, transverse fluctuations, and crossover dynamics of a semi-flexible chain in two dimensions

A Huang, A Bhattacharya, K Binder - The Journal of Chemical Physics, 2014 - pubs.aip.org
We present a unified scaling description for the dynamics of monomers of a semiflexible
chain under good solvent condition in the free draining limit. We consider both the cases …

Linear dimensions of adsorbed semiflexible polymers: What can be learned about their persistence length?

A Milchev, K Binder - Physical Review Letters, 2019 - APS
Conformations of partially or fully adsorbed semiflexible polymer chains are studied varying
both contour length L, chain stiffness, κ, and the strength of the adsorption potential over a …

Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles

A Huang, HP Hsu, A Bhattacharya… - The Journal of chemical …, 2015 - pubs.aip.org
The conformations of semiflexible polymers in two dimensions confined in a strip of width D
are studied by computer simulations, investigating two different models for the mechanism …

Persistence length of poly (vinyl amine): quantitative image analysis versus single molecule force response

S Kozhuharov, M Radiom, P Maroni… - Macromolecules, 2018 - ACS Publications
Single molecules of poly (vinyl amine) are analyzed in the adsorbed state by atomic force
microscopy (AFM) in two different ways. First, high-resolution images of individual adsorbed …