Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Hendrick W de HaanGary W Slater

Abstract

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 relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Péclet control parameter, λ, we are able to correct this and tune the simulations to replicate the experimental P(t) (for dsDNA and other scenarios). To show the effect that a particular P(t) can have on the dynamics of translocation, we perform simulations across a wide range of P(t) values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P(t) brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time ...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
May 1, 1986·Physical Review A: General Physics·G S Grest, K Kremer
Jul 22, 1996·Physical Review Letters·W Sung, P J Park
May 1, 2001·Physical Review Letters·A MellerD Branton
Aug 25, 2004·Biophysical Journal·Jiunn B HengGregory Timp
Aug 11, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A J StormC Dekker
Sep 15, 2005·Nano Letters·Daniel FologeaJiali Li
Sep 24, 2005·Nano Letters·Arnold J StormCees Dekker
Oct 13, 2005·Nano Letters·Daniel FologeaJiali Li
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ilkka HuopaniemiSee-Chen Ying
Mar 5, 2008·The Journal of Chemical Physics·Aslin IzmitliJuan J de Pablo
Aug 19, 2008·Biophysical Journal·Meni WanunuAmit Meller
Mar 5, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·V V LehtolaK Kaski
Aug 12, 2009·The European Physical Journal. E, Soft Matter·A BhattacharyaK Binder
Mar 20, 2010·Nano Letters·Stefan W KowalczykCees Dekker
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·V V LehtolaK Kaski
May 21, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Takahiro Sakaue
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hendrick W de Haan, Gary W Slater
Jan 15, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·V V LehtolaR P Linna
Apr 26, 2011·The Journal of Chemical Physics·Hendrick W de Haan, Gary W Slater
Jul 26, 2011·The Journal of Physical Chemistry. B·Payam Rowghanian, Alexander Y Grosberg
Aug 24, 2011·Macromolecules·Yanwei WangKevin D Dorfman
Jun 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·J L A DubbeldamT A Vilgis
Jun 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·R P Linna, K Kaski
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·T IkonenW Sung
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Takuya Saito, Takahiro Sakaue
Feb 7, 2013·Physical Review Letters·Mirna MihovilovicDerek Stein
May 18, 2013·Physical Review Letters·Liang DaiPatrick S Doyle
Jun 8, 2013·The Journal of Chemical Physics·Ramesh Adhikari, Aniket Bhattacharya
Nov 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Takuya Saito, Takahiro Sakaue
Jun 17, 2014·Nature Communications·Angus McMullenDerek Stein
Jan 25, 2013·Physical Review Letters·Hendrick W de Haan, Gary W Slater
Nov 1, 2004·Nano Letters·Peng ChenDaniel Branton
Oct 3, 2014·The Journal of Chemical Physics·J L A DubbeldamT A Vilgis

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Citations

Jun 17, 2014·Nature Communications·Angus McMullenDerek Stein
Jul 18, 2018·Physical Review. E·P M Suhonen, R P Linna
Sep 27, 2018·Physical Review. E·Hendrick W de HaanGary W Slater
Nov 10, 2018·The Journal of Chemical Physics·Martin MagillHendrick W de Haan
Feb 10, 2017·The Journal of Chemical Physics·David Sean, Gary W Slater
Mar 16, 2018·Physical Review Letters·Angus McMullenDerek Stein
Jan 15, 2018·The Journal of Chemical Physics·H H Katkar, M Muthukumar
Nov 1, 2017·Nano Letters·Kyle BriggsVincent Tabard-Cossa

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