Electrostatic/entropic macromolecule manipulation in nanochannel. Swapping of macromolecule locations

Abstract

Evolution of a polyion and an electrically uncharged macromolecule in confined environment, represented by a tight nanopore, induced by external electric field, is investigated. The motion of the uncharged macromolecule is forced by the polyion. In suitably selected conditions, the collision between macromolecules, compression of the uncharged macromolecule, and finally the swap of positions of macromolecules in the nanochannel are observed by means of the nonequilibrium Monte Carlo method on the lattice. The exemplary trajectories of macromolecules, their geometry, and energetics are analyzed. The dependence of the time of swapping on the number of macromolecule beads is described by scaling laws.

Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries

“…Numerous computer simulation studies have examined the effects of entropic repulsion for two polymers in such geometries. 1–23 Most of these studies have examined the segregation behaviour of flexible linear polymers, 1–6,8,9,11,13,16,17 though some have also investigated the behaviour of ring polymers 7,10,12,14,15,18 and more complex topologies. 22,23 In addition, the effects of bending rigidity, 11,16 a difference in the contour lengths, 21 macromolecular crowding, 12,15,18 and electrostatics 19,20 on the segregation dynamics and thermodynamics have been examined in detail.…”

“…1–23 Most of these studies have examined the segregation behaviour of flexible linear polymers, 1–6,8,9,11,13,16,17 though some have also investigated the behaviour of ring polymers 7,10,12,14,15,18 and more complex topologies. 22,23 In addition, the effects of bending rigidity, 11,16 a difference in the contour lengths, 21 macromolecular crowding, 12,15,18 and electrostatics 19,20 on the segregation dynamics and thermodynamics have been examined in detail. Information gleaned from these studies may be useful in helping advance nanofluidic technology used in applications such as DNA sorting, 24 DNA denaturation mapping, 25,26 and genome mapping.…”

Free energy and segregation dynamics of two channel-confined polymers of different length

“…This process has been the subject of numerous theoretical and computer simulation studies in recent years. [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] Most of these studies have examined the segregation behavior of flexible linear polymers, [4][5][6][7][8][9]11,12,14,16,19,20 though some have also investigated the behavior of ring polymers. 10,13,15,17,18,21 In addition, the effects of of bending rigidity, 14,19 macromolecular crowding, 15,18,21 and electrostatics 22,23 on the segregation dynamics and thermodynamics have been examined in detail.…”