57 citations · 148 across the 8 of their papers we have counts for
6 papers · 1 filter
Waves of DNA: Propagating Excitations in Extended Nanoconfined Polymers
Alexander R. Klotz, Hendrick W. de Haan, Walter W. Reisner
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined i…
Force-Extension for DNA in a Nanoslit: Using an Effective Dimensionality to Map between the 3D and 2D Limits
Hendrick W. de Haan, Tyler N. Shendruk
The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form…
Coarse-Grained Molecular Dynamics Simulations of Depletion-Induced Interactions for Soft Matter Systems
Tyler N. Shendruk, Martin Bertrand, James L. Harden +2
Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for…
Simulating the Entropic Collapse of Coarse-Grained Chromosomes
Tyler N. Shendruk, Martin Bertrand, Hendrick W. de Haan +2
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromoso…
Using a Péclet Number for the Translocation of Polymer through a Nanopore to Tune Coarse-Grained Simulations to Experimental Conditions
Hendrick W. de Haan, David Sean, Gary W. Slater
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relativ…
Translocation of a Polymer through a Nanopore across a Viscosity Gradient
Hendrick W. de Haan, Gary W. Slater
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer ha…