Related papers: Electrophoresis of positioned nucleosomes
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…
DNA translocation through nanopores is one of the most promising strategies for the next-generation sequencing technologies. Most part of experimental and numerical works has focused on polymer translocation biased by electrophoresis, where…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
A system of reduced equations is proposed for the electron motion in the strongly-radiation dominated regime for an arbitrary electromagnetic field configuration. The developed approach is used to analyze various scenarios of an electron…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We investigate the translocation of rods with different charge distributions using hybrid Langevin Dynamics and Lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the $P^3M$ algorithm to model…
We generalize the compact group approach to conducting systems to give a self-consistent analytical solution to the problem of the effective quasistatic electrical conductivity of macroscopically homogeneous and isotropic dispersions of…
This work presents a microscale approach for simulating the dielectrophoresis (DEP) assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as…
Coarse (<=20 micron) titanium particles were deposited on low-carbon steel substrates by cathodic electrophoretic deposition (EPD) with ethanol as suspension medium and poly(diallyldimethylammonium chloride) (PDADMAC) as polymeric charging…
We present a novel theory and implementation for computing coupled electronic and quantal nuclear subsystems on a single potential energy surface, moving beyond the standard Born-Oppenheimer (BO) separation of nuclei and electrons. We…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Hydrogen bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which…
A fully consistent model to study electrodynamics for superconductors in the stationary and non-stationary regime has been developed based on Proca equations and a massive photon. In particular, this approach has been applied to study the…
Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
By molecular dynamics simulation, we study the charge inversion phenomenon of a rod macroion in the presence of polyelectrolyte counterions. We simulate electrophoresis of the macroion under an applied electric field. When both counterions…