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The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Normal and anomalous diffusion are ubiquitous in many complex systems [1] . Here, we define a time and space generalized diffusion equation (GDE), which uses fractional-time derivatives and transformed d-path Laplacian operators on…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
We investigate dynamical transport properties of interacting electrons moving in a vibrating nanoelectromechanical wire in a magnetic field. We have built an exactly solvable model in which electric current and mechanical oscillation are…
Strongly interacting electron systems can provide insight into quantum many-body phenomena, such as Mott insulating behavior and spin liquidity, facilitating semiconductor optimization. The Fermi-Hubbard model is the prototypical model used…
A first-principles coupled electron-nuclear dynamics simulation based on real-time, time-dependent density functional theory and Ehrenfest dynamics quantitatively repro-duces bimodal translational energy loss and angular distributions…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
By means of the concept of factorial moment the charge transfer rates in DNA segments with fractal structures are investigated. An analytical form for the electron transfer rate is obtained.
Chiral-induced-spin-selectivity of electron transport and its interplay with DNA's mechanical motion is explored in a double stranded DNA helix with spin-orbit-coupling. The mechanical degree of freedom is treated as a stochastic classical…
Electron transport characteristics are investigated through some molecular chains attached to two non-superconducting electrodes by the use of Green's function method. Here we do parametric calculations based on the tight-binding…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Motivated by novel results in the theory of correlated sequences, we analyze the dynamics of random walks with long-term memory (binary chains with long-range correlations). In our model, the probability for a unit bit in a binary string…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The fundamental equations of particle motion lead to a modified Poisson equation including dynamic charge. This charge derives from density oscillations of a particle; it is not discrete, but continuous. Within the dynamic model of hydrogen…
Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have…