arXiv subjects

Simone Melchionna

Publications and source records attributed to Simone Melchionna.

39 records · Page 3Linked to original sources

arXiv2007

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

We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent dynamics. A unique feature of the present approach is that hydrodynamic interactions between the solute macromolecule and the aqueous solvent are handled explicitly, and yet in a computationally tractable way due to the dual particle-field nature of the LB solver. The suitability of the present LB-MD multiscale approach is demonstrated for the problem of polymer fast translocation through a nanopore. We also provide an interpretation of our results in the context of DNA translocation through a nanopore, a problem that has attracted much theoretical and experimental attention recently.

physics.bio-ph↗

arXiv2005

Solving the Fokker-Planck kinetic equation on a lattice

We propose a discrete lattice version of the Fokker-Planck kinetic equation along lines similar to the Lattice-Boltzmann scheme. Our work extends an earlier one-dimensional formulation to arbitrary spatial dimension $D$. A generalized Hermite-Gauss procedure is used to construct a discretized kinetic equation and a Chapman-Enskog expansion is applied to adapt the scheme so as to correctly reproduce the macroscopic continuum equations. The stability of the algorithm with respect to the finite time-step $Δt$ is characterized by the eigenvalues of the collision matrix. A heuristic second-order algorithm in $Δt$ is applied to investigate the time evolution of the distribution function of simple model systems, and compared to known analytical solutions. Preliminary investigations of sedimenting Brownian particles subjected to an orthogonal centrifugal force illustrate the numerical efficiency of the Lattice-Fokker-Planck algorithm to simulate non-trivial situations. Interactions between Brownian particles may be accounted for by adding a standard BGK collision operator to the discretized Fokker-Planck kernel.

cond-mat.stat-mech↗

arXiv2002

Intermittent permeation of cylindrical nanopores by water

Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding material. At threshold, the permeation is {\emph{intermittent}} on a nanosecond timescale, and strongly enhanced by the presence of an ion inside the channel, providing a possible mechanism for gating. Confined water remains surprisingly fluid and bulk-like. Its behaviour differs strikingly from that of a reference Lennard-Jones fluid, which tends to contract into a highly layered structure inside the channel.

cond-mat.soft↗