Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

Abstract

Simulation of DNA electrophoresis facilitates the design of DNA separation devices. Various methods have been explored for simulating DNA electrophoresis and other processes using implicit and explicit solvent models. Explicit solvent models are highly desired but their applications may be limited by high computing cost in simulating large number of solvent particles. In this work, a coarse-grained hybrid molecular dynamics (CGH-MD) approach was introduced for simulating DNA electrophoresis in explicit solvent of large number of solvent particles. CGH-MD was tested in the simulation of a polymer solution and computation of nonuniform charge distribution in a cylindrical nanotube, which shows good agreement with observations and those of more rigorous computational methods at a significantly lower computing cost than other explicit-solvent methods. CGH-MD was further applied to the simulation of DNA electrophoresis in a polymer solution and in a well-studied nanofluidic device. Simulation results are consistent with observations and reported simulation results, suggesting that CGH-MD is potentially useful for studying electrophoresis of macromolecules and assemblies in nanofluidic, microfluidic, and microstructure array systems that involve extremely large number of solvent particles, nonuniformly distributed electrostatic interactions, bound and sequestered water molecules.

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

“…This requires a very large number of particles (and a very big number of degree of freedom) if using molecular dynamics simulation. To reduce the number of degrees of freedom, coarse-grained molecular dynamic techniques have been developed [58,[65][66][67].…”

“…While DPD is not as computationally efficient as lattice Boltzmann simulations, it is a more flexible method that does not suffer from the numerical instability associated with many lattice Boltzmann applications. DPD facilitates the simulation of complex fluid systems on physically interesting and important length and time scales, including bio-particle and DNA filtering systems [56][57][58].…”

A scalable multiphysics algorithm for massively parallel direct numerical simulations of electrophoretic motion

“…Thus, [101] suggest to use the forcing term (40) in combination with the modified momentum density definition in Eqn. (41) for the BGK.…”

“…The mesoscale dissipative particle dynamics method is applied in [39] to simulate electrophoresis of a polyelectrolyte in a nanochannel. Another explicit solvent method is presented in [40] for simulating DNA electrophoresis, modeling DNA as a polymer. In both methods the polymer is represented by bead-spring chains with beads represented by a truncated Lennard-Jones potential and connected by elastic spring potentials.…”

“…In both methods the polymer is represented by bead-spring chains with beads represented by a truncated Lennard-Jones potential and connected by elastic spring potentials. Explicit solvent models, however, are computationally very expensive, especially for large numbers of fluid molecules due to pairwise interactions [40]. Moreover, the resolution of solvent, macromolecules, and ions on the same scale limits the maximal problem sizes that can be simulated [41].…”