The potential and challenges of nanopore sequencing

D Branton, DW Deamer, A Marziali, H Bayley… - Nature …, 2008 - nature.com
A nanopore-based device provides single-molecule detection and analytical capabilities
that are achieved by electrophoretically driving molecules in solution through a nano-scale …

Polymer translocation: the first two decades and the recent diversification

VV Palyulin, T Ala-Nissila, R Metzler - Soft matter, 2014 - pubs.rsc.org
Probably no other field of statistical physics at the borderline of soft matter and biological
physics has caused such a flurry of papers as polymer translocation since the 1994 …

Polymer translocation and nanopore sequencing: a review of advances and challenges

SL Singh, K Chauhan, AS Bharadwaj… - International Journal of …, 2023 - mdpi.com
Various biological processes involve the translocation of macromolecules across
nanopores; these pores are basically protein channels embedded in membranes …

Influence of polymer-pore interactions on translocation

K Luo, T Ala-Nissila, SC Ying, A Bhattacharya - Physical Review Letters, 2007 - APS
We investigate the influence of polymer-pore interactions on the translocation dynamics
using Langevin dynamics simulations. An attractive interaction can greatly improve the …

Sucking genes into pores: Insight into driven translocation

T Sakaue - Physical Review E—Statistical, Nonlinear, and Soft …, 2010 - APS
Flexible polymers such as long DNA, RNA molecules, and proteins, can pass through a
narrow pore whose size is comparable to their molecular thickness. We highlight the …

Unifying model of driven polymer translocation

T Ikonen, A Bhattacharya, T Ala-Nissila, W Sung - Physical Review E …, 2012 - APS
We present a Brownian dynamics model of driven polymer translocation, in which
nonequilibrium memory effects arising from tension propagation (TP) along the cis side …

Sequence dependence of DNA translocation through a nanopore

K Luo, T Ala-Nissila, SC Ying, A Bhattacharya - Physical Review Letters, 2008 - APS
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin
dynamics simulations, focusing on the dependence of the translocation dynamics on the …

Modeling the separation of macromolecules: A review of current computer simulation methods

GW Slater, C Holm, MV Chubynsky… - …, 2009 - Wiley Online Library
Abstract Theory and numerical simulations play a major role in the development of improved
and novel separation methods. In some cases, computer simulations predict counterintuitive …

Driven polymer translocation through nanopores: Slow-vs.-fast dynamics

K Luo, T Ala-Nissila, SC Ying, R Metzler - Europhysics letters, 2010 - iopscience.iop.org
We investigate the dynamics of polymer translocation through nanopores under external
driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average …

Influence of non-universal effects on dynamical scaling in driven polymer translocation

T Ikonen, A Bhattacharya, T Ala-Nissila… - The Journal of chemical …, 2012 - pubs.aip.org
We study the dynamics of driven polymer translocation using both molecular dynamics (MD)
simulations and a theoretical model based on the non-equilibrium tension propagation on …