Timo Ikonen

Influence of pore friction on the universal aspects of driven polymer translocation

T. Ikonen, A. Bhattacharya, T. Ala-Nissila, 3 and W. Sung Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA Department of Physics, Box 1843, Brown University, Providence, Rhode Island 02912-1843 Department of Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea (Dated: November 26, 2012)We derive a scaling ansatz for the mean first passage time (MFPT) τ of a driven polymer chain through a nanopore as a function of the chain length N, the external bias f, and the effective pore-polymer friction η, and demonstrate that the pore-polymer interaction, which we introduce as a correction term to asymptotic scaling, is responsible for the dominant finite-size effect. This ansatz provides a simple procedure to extract the asymptotic τ in the large-N limit from a finite chain length data (obtained either from experiment or simulation) by eliminating the correction-to-scaling term. We validate the ansatz applying it on a large set of data for τ obtained using Brownian dynamics (BD) and Brownian dynamics tension propagation (BDTP) simulation results (Ikonen T. et al., Phys. Rev. E, 85 (2012) 051803; J. Chem. Phys., 137 (2013) 085101) for a variety of combination for N, f, and η. As an important practical application we demonstrate how the rescaling procedure can be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we extend the BDTP theory to incorporate Zimm dynamics and find that the asymptotic results for τ (or the translocation exponent) remains unaltered with the inclusion of the hydrodynamics interactions (HI), although the convergence is slower than what we observe for Rouse dynamics. Using the rescaling ansatz we find that these new findings are in good agreement with the existing experimental results as well as with lattice Boltzmann results for driven polymer translocation (PT) for small N.

Iso-flux tension propagation theory of driven polymer translocation: the role of initial configurations.

We investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of motion for the tension front. From this we derive a scaling relation for the average translocation time τ, which captures the asymptotic result τ∝N0(1+ν), where N0 is the chain length and ν is the Flory exponent. In addition, we derive the leading correction-to-scaling term to τ and show that all terms of order N0(2ν) exactly cancel out, leaving only a finite-chain length correction term due to the effective pore friction, which is linearly proportional to N0. We use the model to numerically include fluctuations in the initial configuration of the polymer chain in addition to thermal noise. We show that when the cis side fluctuations are properly accounted for, the model not only reproduces previously known results but also considerably improves the estimates of the monomer waiting time distribution and the time evolution of the translocation coordinate s(t), showing excellent agreement with MD simulations.

Driven translocation of a semi-flexible polymer through a nanopore

We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory, and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length

Driven polymer transport through a periodically patterned channel.

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Comparison of global sensitivity analysis methods – Application to fuel behavior modeling

ℓ˜p the trans side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance RN as a function of the chain length N must be known. To this end, we first derive a semi-analytic scaling form for RN, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the trans side friction based on MD simulations. Augmented with these two factors, the theory shows that there are three main regimes for the scaling of the average translocation time τ ∝ Nα. In the rod

Module for thermomechanical modeling of LWR fuel in multiphysics simulations

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