Related papers: Electrophoresis of positioned nucleosomes
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
We present for the first time a complex network approach to the study of the electrical properties of single protein devices. In particular, we consider an electronic nanobiosensor based on a G-protein coupled receptor. By adopting a coarse…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Nonlinear field dependence of electrophoresis in high fields has been investigated theoretically, yet experimental studies have failed to reach consensus on the effect. In this work, we present a systematic study on the nonlinear…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
The past decade has witnessed tremendous progress in the theoretical and computational tools that produce our understanding of nuclei. A number of microscopic calculations of nuclear electroweak structure and reactions have successfully…
We derive and solve by the spectral method the equations for a neutral system of ultra-relativistic electrons that are compressed to the radius of the nucleus and subject to a driving force. This driving force can be thought of as…
Both the translational diffusion coefficient $D$ and the electrophoretic mobility $\mu$ of a short rod-like molecule (such as dsDNA) that is being pulled towards a nanopore by an electric field should depend on its orientation. Since a…
In this work we present a new method of approximating the continuum wavefunctions with a discrete basis set. This method aims to be at least compatible with other well known methods of the electronic structure theory to describe processes…
Nanoscopic heterogeneities in composition and structure are quintessential for the properties of electrocatalyst materials. Here, we present a semiclassical model to study the electrochemical properties of supported electrocatalyst…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
Electrophoretic separations of proteins are widely used in proteomic analyses, and rely heavily on SDS electrophoresis. This mode of separation is almost exclusively used when a single dimension separation is performed, and generally…
We present a new formulation to calculate the electric conductance of mesoscopic conductors by utilizing the singular value decomposition, which is a mathematical technique to manipulate matrices. Our formulation is useful in treating…
The electrophoretic mobility of a spherical particle is well understood, yet how particle shape modifies this mobility at arbitrary Debye length remains an open question. Here, we compute the electrophoretic mobility of a nearly spherical…
We study electrostatic interaction between molecules of the DNA in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a…
Micro-Electro-Mechanical Systems (MEMS) normally have fixed or moving structures (plates or array of thin beams) with cross-sections of the order of microns and lengths of the order of tens or hundreds of microns. Electrostatic forces play…
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples…
A novel mathematical treatment is proposed for computing the time evolution of dynamic nuclear polarization processes in the low temperature thermal mixing regime. Without assuming any a priori analytical form for the electron polarization,…