57 citations · 148 across the 8 of their papers we have counts for
8 papers
Studying First Passage Problems using Neural Networks: A Case Study in the Slit-Well Microfluidic Device
Andrew M. Nagel, Martin Magill, Hendrick W. de Haan
This study presents deep neural network solutions to a time-integrated Smoluchowski equation modeling the mean first passage time of nanoparticles traversing the slit-well microflu…
Neural Network Solutions to Differential Equations in Non-Convex Domains: Solving the Electric Field in the Slit-Well Microfluidic Device
Martin Magill, Andrew M. Nagel, Hendrick W. de Haan
The neural network method of solving differential equations is used to approximate the electric potential and corresponding electric field in the slit-well microfluidic device. The…
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…