Related papers: Electronic Conduction in Short DNA Wires
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…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
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 report transport properties and particle current rectification operation in a double-stranded tight-binding ladder network within non-equilibrium Green's function (NEGF) formalism that can easily be generalized in multi-stranded systems.…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Recent advances in experimental techniques emphasize the usefulness of multiple scanning probe techniques when analyzing nanoscale samples. Here, we analyze theoretically dual-probe setups with probe separations in the nanometer range,…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
We use the non-equilibrium Green's function formalism along with a self-consistent Hartree-Fock approximation to numerically study the effects of a single impurity and interactions between the electrons (with and without spin) on the…
We show experimentally that a cheap glass microcapillary can accumulate {\lambda}-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
We identify experimental signatures in the current-voltage (I-V) characteristics of weakly contacted molecules directly arising from excitations in their many electron spectrum. The current is calculated using a multielectron master…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
Density functional calculations for the electronic conductance of single molecules are now common. We examine the methodology from a rigorous point of view, discussing where it can be expected to work, and where it should fail. When…
We study the electrostatic potential of a molecular wire bridging two metallic electrodes in the limit of weak contacts. With the use of a tight-binding model including a fully three-dimensional treatment of the electrostatics of the…
We present an efficient method for evaluating current-induced forces in nanoscale junctions, which naturally integrates into the non-equilibrium Green's function formalism implemented within density functional theory. This allows us to…
The coupling of the charge carriers passing through a molecule bridging two bulky conductors with local vibrational modes of the molecule, gives rise to distinct features in the electronic transport properties on one hand, and to…