arXiv subjects

Rouhollah Haji Abdolvahab

Publications and source records attributed to Rouhollah Haji Abdolvahab.

3 recordsLinked to original sources

arXiv2019

Translocation through a narrow pore under a puling force

We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces. In order to see the polymer and pore interaction effects on translocation time, we studied 9 different interaction energies. Moreover, to better understand the simulation results we investigate polymer center of mass, shape factor and the monomer distribution through the translocation. Our results unveil that while increasing the polymer-pore interaction energy slows down the translocation, expanding the pore diameter, makes the translocation faster. The shape analysis of the results reveals that the polymer shape is very sensitive to the interaction energy. In high interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last.

physics.comp-ph↗

arXiv2018

Effects of interaction between nanopore and polymer on translocation time

Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8k_B T is smaller from the non-equilibrium case even in the small energy of 1k_B T.

physics.comp-ph↗

arXiv2016

Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy

Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, $β$ ($T\simβ$). Interestingly in some special cases e.g. chaperones of size $λ=6$ and with exponential distribution rate of $α=5$, the minimum reaches even to amount of less than $1$ ($β<1$). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into account the velocity dependency of the translocation on polymer length, one could truly predict the amount of this minimum.

physics.bio-ph↗