Nanopores

The passage of a polymer across a membrane through a constricting passage way is central to many biological processes: transport of proteins across cells, DNA packing into cells, etc. Further, with recent advances in nanofabrication, it is now possible to manufacture solid state nanopores that are able to confine individual DNA strands. With these applications in mind, we are using a variety of simulation techniques to both carefuly quantify the dynamics of translocation and to examine the process in novel setups.

Related Manuscripts:

Kyle Briggs, Gregory Madejski, Martin Magill, Konstantinos Kastritis, Hendrick W de Haan, James L McGrath, and Vincent Tabard-Cossa,"DNA Translocations Through Nanopores Under Nanoscale Pre-Confinement", Nano Letters, 10.1021/acs.nanolett.7b03987 (2017).

Magill M, Falconer C, Waller E, de Haan HW,"Translocation Time through a Nanopore with an Internal Cavity Is Minimal for Polymers of Intermediate Length", Physical Review Letters, 117, 247802 (2016).

Vollmer S, de Haan HW,"Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore", Journal of Chemical Physics, 145, 154902 (2016).

de Haan HW, Sean D, Slater GW, "Using a Peclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions", Physical Review E., 91, 022601 (2015).

Sean D, de Haan HW, Slater GW, "Translocation of a Polymer Through a Nanopore Starting From a Confining Nanotube", Electrophoresis, 36(5):682-91 (2015).

de Haan HW, Slater GW, "Biomolecule transport across biomembranes in the presence of crowding: Polymer translocation driven by concentration and disorder gradients", Physical Review E (Rapid Communication), 90, 020601(R) (2014).

McMullen A, de Haan HW, Tang JX, Stein D, "Stiff filamentous virus translocations through solid-state nanopores", Nature Communications, 5, 4171 (2014).

de Haan HW, Slater GW, "Translocation of a Polymer through a Nanopore across a Viscosity Gradient", Physical Review E, 87(4), 042604 (2013).

de Haan HW, Slater GW, "Translocation of a polymer through a nanopore modulated by a sticky site", Journal of Chemical Physics, 138(9), 094906 (2013).

de Haan HW, Slater GW, "Translocation of "rod-coil" polymers: probing the structure of single molecules within nanopores", Physical Review Letters, 110(4), 048101 (2013).

de Haan HW, Slater GW, "Using an Incremental Mean First Passage Approach to Explore the Viscosity Dependent Dynamics of the Unbiased Translocation of a Polymer through a Nanopore", Journal of Chemical Physics, 136(20), 204902 (2012).

de Haan HW, Slater GW, "Memory effects during the unbiased translocation of a polymer through a nanopore", Journal of Chemical Physics, 136(5), 154903 (2012).

de Haan HW, Slater GW, "An incremental mean first passage analysis for a quasistatic model of polymer translocation through a nanopore", Journal of Chemical Physics, 134, 154905 (2011).

de Haan HW, Gauthier MG, Chubynsky MV, Slater GW, "The Importance of Introducing a Waiting Time for Lattice Monte Carlo Simulations of a Polymer Translocation Process", Computer Physics Communications, 182(1), 29-32 (2011).

de Haan HW, Slater GW, "Mapping the Variation of the Translocation alpha Scaling Exponent with Nanopore Width", Physical Review E, 81(5), 051802 (2010).

Slater GW, Holm C, Chubynsky MV, de Haan HW, Dube A, Grass K, Hickey OA, Kingsburry C, Sean D, Shendruk TN, Zhan L, "Modeling the separation of macromolecules: a review of current computer simulation methods", Electrophoresis, 30(5), 792-818 (2009).

      Hendrick de Haan : hendrick.dehaan@uoit.ca       ||       faculty.uoit.ca/dehaan/cNAB.LAB