Related papers: Electrophoresis of positioned nucleosomes
We discuss the repton model of agarose gel electrophoresis of DNA. We review previous results, both analytic and numerical, as well as presenting a new numerical algorithm for the efficient simulation of the model, and suggesting a new…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Electrophoresis is the motion of particles relative to a surrounding fluid driven by a uniform electric field. In conventional electrophoresis, the electrophoretic velocity grows linearly with the applied field. Nonlinear effects with a…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We present two models for electron-driven uphill proton transport across lipid membranes, with the electron energy converted to the proton gradient via the electrostatic interaction. In the first model, associated with the cytochrome c…
Polymer electrolytes (PEs) are promising candidates for use in next-generation high-voltage batteries, as they possess advantageous elastic and electrochemical properties. However, PEs still suffer from low ionic conductivity and need to be…
The electrostatic contribution to twist rigidity of DNA is studied, and it is shown that the Coulomb self-energy of the double-helical sugar-phosphate backbone contributes considerably to twist rigidity of DNA--the electrostatic twist…
Electron transport within nanostructures can be important to varied engineering applications, such as thermoelectrics and nanoelectronics. In theoretical studies, electron Monte Carlo simulations are widely used as an alternative approach…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
We use a hydrodynamic reciprocal approach to phoretic motion to derive general expressions for the electrophoretic and thermophoretic mobility of weakly charged colloids in aqueous electrolyte solutions. Our approach shows that phoretic…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
When electrolyte solutions are confined in micro- and nanochannels their conductivity is significantly different from those in a bulk phase. Here we revisit the theory of this phenomenon by focusing attention on the reduction in the ion…
We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed…
Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a…
The electrical properties of DNA molecules are investigated by charge injection and electric force microscopy experiments. Prior to injection, DNA molecules exhibit a weak positively charged state. We probe the electrical behaviour of DNA…
A crucial factor determining charge transport in organic semiconductors is the electronic coupling between the molecular constituents, which is heavily influenced by the relative arrangement of the molecules. This renders quinacridone, with…