Related papers: Electrophoresis of positioned nucleosomes
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
In this work, we use Molecular Dynamics and Lattice-Boltzmann simulations to study the properties of charged Janus particles in an electric field. We show that for relatively small net charge and thick electrostatic diffuse layer mobilities…
We present mesoscopic DPD-simulations of polyelectrolyte electrophoresis in confined nanogeometries, for varying salt concentration and surface slip conditions. Special attention is given to the influence of electroosmotic flow (EOF) on the…
We study the mobility of a charged colloidal particle in a constant homogeneous electric field by means of computer simulations. The simulation method combines a lattice Boltzmann scheme for the fluid with standard Langevin dynamics for the…
Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong…
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We use a coarse-grained molecular dynamics model to study the electrophoretic behaviour of flexible polyelectrolyte chains. We first characterize the static properties of the model with respect to the chain length, the polyelectrolyte…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We study the electrophoretic mobility of spherical charged colloids in a low-salt suspension as a function of the colloidal concentration. Using an effective particle charge and a reduced screening parameter, we map the data for systems…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
A simple formula is obtained for coupling electrons in a complex system to the electromagnetic field. It includes the effect of intra-atomic excitations and nuclear motion, and can be applied in. e.g., first-principles-based simulations of…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Periodic arrays of micro- or nano-pillars constitute solid state matrices with excellent properties for DNA size separation. Nanofabrication technologies offer many solutions to tailor the geometry of obstacle arrays, yet most studies have…
Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution…
We calculate the thermophoretic drift of a charged single colloidal particle with hydrodynamically slipping surface immersed in an electrolyte solution in response to a small temperature gradient. Here, we rely on a linearized hydrodynamic…
We present quantitative results for the drift velocity of a polymer in a gel if a force (e.g. through an electric or magnetic field) acts on a tag, attached to one of its ends. This is done by introducing a modification of the…
We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force…
We investigate the dielectrophoretic motion of charge-neutral, polarizable nanocolloids through molecular dynamics simulations. Comparison to analytical results derived for continuum systems shows that the discrete charge distributions on…
Numerical solutions of the standard electrokinetic model provide a basis for interpreting a variety of electrokinetic phenomena involving `bare' colloids. However, the model rests on the classical notion of a shear or slipping plane, whose…