Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore

Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the \textit{trans}-side. Under the influence of pre-stretching forces, the elongated polymer ensemble contains less variations in conformation...

We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses ca...

The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the polyelectrolyte and the fluid, a coarse-grained molecular dynamics model connected to a mesoscopic fluid described by the Lattice Boltzmann approach is used to investigate free-solution electrophoresis. Our study demonstrates the importance of hyd...

We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model DNA segment by evaluating the potential of mean force in absence and presence of polarization effects by means of coarse-grained molecular dynamics simulations. The effect of induced polarization charges has been taken into account by empl...

We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This is found to have an impact on both the translocation time as a function of the chain length and on the polymer entry frequency. We qualitatively compare our results to available experimental data.

Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the merging of two black holes at a distance of 1.3 billion light-years from Earth, and the very small, such as the identification of individual viral particles from a complex mixture. This dissertation is devoted to studying the physical mechanisms ...

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...

A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the appropriate mapping of length and time units from LB to MD, the velocity field as obtained from MD is quantitatively reproduced by LB. The implications of this finding for prospective LB-MD multiscale applications are discussed.

Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter $R$ through a nanopore under a driving force $F$. Due to the crowding effect induced by the partially translocated monomers, the translocation dynamics is significantly altered in comparison to an unconfined environment, namely, we observe a nonuniversal dependence of the translocation time $\tau$ on the chain length $N$. $\tau$ initia...

DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observ...