Related papers: Electrophoresis of positioned nucleosomes
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
We discuss the electrostatic contribution to the elastic moduli of a cell or artificial membrane placed in an electrolyte and driven by a DC electric field. The field drives ion currents across the membrane, through specific channels, pumps…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We consider electrophoresis of a single charged colloidal particle in a finite box with periodic boundary conditions, where added counterions and salt ions ensure charge neutrality. A systematic rescaling of the electrokinetic equations…
A model is described, in which electrical breakdown in high-voltage systems is caused by stochastic fluctuations of the mobile dislocation population in the cathode. In this model, the mobile dislocation density normally fluctuates, with a…
We introduce an analytical method to generate the pathway of a closed protein-bound DNA minicircle. This is a general method which can be used to connect any two open curves with well defined mathematical definitions as well as pairs of…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Understanding the electrodes' surface morphology influence on the ions' distribution is essential for designing the supercapacitors with enhanced energy density characteristics. We develop a model for the structure of electrolytes near the…
We investigate the behavior of single polyelectrolytes in multivalent salt solutions under the action of electric fields through computer simulations. The chain is unfolded in a strong electric field and aligned parallel to the field…
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
A wide range of ultrafast phenomena in various atomic, molecular and condense matter systems is governed by electron dynamics. Therefore, the ability to image electronic motion in real space and real time would provide a deeper…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The rising demand for high-performing batteries requires new technological concepts. To facilitate fast charge and discharge, hierarchically structured electrodes offer short diffusion paths in the active material. However, there are still…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
Electromagnetic properties of the nucleon are explored with lattice QCD using a novel technique. Focusing on background electric fields, we show how the electric polarizability can be extracted from nucleon correlation functions. A crucial…