Journal ArticleDOI
Barrier crossing in one and three dimensions by a long chain
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In this article, the authors considered the Kramers problem for a long chain polymer trapped in a biased double-well potential and showed that the time of crossing is proportional to the chain length, which is in agreement with the results for the kink mechanism.Abstract:
We consider the Kramers problem for a long chain polymer trapped in a biased double-well potential Initially the polymer is in the less stable well and it can escape from this well to the other well by the motion of its N beads across the barrier to attain the configuration having lower free energy In one dimension we simulate the crossing and show that the results are in agreement with the kink mechanism suggested earlier In three dimensions, it has not been possible to get an analytical 'kink solution' for an arbitrary potential; however, one can assume the form of the solution of the nonlinear equation as a kink solution and then find a double-well potential in three dimensions To verify the kink mechanism, simulations of the dynamics of a discrete Rouse polymer model in a double well in three dimensions are carried out We find that the time of crossing is proportional to the chain length, which is in agreement with the results for the kink mechanism The shape of the kink solution is also in agreement with the analytical solution in both one and three dimensionsread more
Citations
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Driven Polymer Translocation Through a Narrow Pore
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Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment
Christian L. Vestergaard,Morten Bo Lindholm Mikkelsen,Walter Reisner,Walter Reisner,Anders Kristensen,Henrik Flyvbjerg +5 more
TL;DR: This work applies transition state theory to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field.
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Transition state theory approach to polymer escape from a one dimensional potential well.
TL;DR: TST with dynamical corrections based on short time trajectories started at the transition state gives rate constant estimates that agree within a factor of two with the molecular dynamics simulations over a wide range of bead coupling constants and polymer lengths.
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Dynamics of polymer translocation through a nanopore under an applied external field
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Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier
TL;DR: In this paper, an efficient method for evaluating the recrossing correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product is presented.
References
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Journal ArticleDOI
Driven polymer translocation through a narrow pore.
TL;DR: In this article, a polynucleotide is driven through a proteinaceous pore by an electric field, and the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions is studied.
Journal ArticleDOI
Driven Polymer Translocation Through a Narrow Pore
TL;DR: There is a range of polymer lengths in which the system is approximately translationally invariant, and a coarse-grained description of this regime is developed, and general features of the distribution of times for the polymer to pass through the pore may be deduced.
Journal ArticleDOI
Translocation of a confined polymer through a hole.
TL;DR: Monte Carlo simulation data collected in the high salt limit (nu approximately 3/5) are in agreement with the asymptotic law and provide vivid details of the escape.
Journal ArticleDOI
Anomalous dynamics of translocation.
TL;DR: The results indicate that for large N, translocation times scale in the same manner as diffusion times, but with a larger prefactor that depends on the size of the hole, which implies anomalous dynamics for the translocation process.
Journal ArticleDOI
Kinetics of duplex formation for individual DNA strands within a single protein nanopore
TL;DR: Details of the kinetics difficult to obtain by conventional methods, like surface plasmon resonance, which measure ensemble properties are revealed by investigating the temperature dependence of DNA duplex formation at the single molecule level.
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