Related papers: Strong Localization of Positive Charge in DNA
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
We have investigated few-body states in vertically stacked quantum dots. Due to small inter-dot tunneling rate, the coupling in our system is in a previously unexplored regime where electron-hole exchange is the dominant spin interaction.…
The effect of mispair on charge transport in a DNA of sequence (GC)(TA)_N(GC)_3 connected to platinum electrodes is studied using the tight-binding model. With parameters derived from ab initio density functional result, we calculate the…
Electron transfer (ET) in biological molecules such as peptides and proteins consists of electrons moving between well defined localized states (donors to acceptors) through a tunneling process. Here we present an analytical model for ET by…
Force fields uniquely assign interatomic forces for a given set of atomic coordinates. The underlying assumption is that electrons are in their quantum-mechanical ground state or in thermal equilibrium. However, there is an abundance of…
Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
In this work we investigate the interplay between coherent and incoherent charge transport in cytosine-guanine (GC) rich DNA molecules. Our objective is to introduce physically grounded approach to dephasing in large molecules and to…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…
Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence…
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…
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 investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
We study the transport of charge due to polarons in a model of DNA which takes in account its 3D structure and the coupling of the electron wave function with the H--bond distortions and the twist motions of the base pairs. Perturbations of…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
We report on our calculations of the inner-sphere reorganization energy and the interaction of the pi orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base…