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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…
It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an…
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 analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
Recently, some authors have shown that a DNA molecule produces electromagnetic signals and communicates with other DNA molecules or other molecules. In fact, a DNA acts like a receiver or transmitter of radio waves. In this paper, we…
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…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
In our report we consider two weakly coupled Schr\"odinger equations as a model of the interchain energy transport in the DNA double-helix. We use the reduction of the Yakushevich-type model considering the torsional dynamics of the DNA. In…
We present a time-dependent study of electron transport through a strongly correlated quantum dot. The time-dependent current is obtained with the multiple-probe battery method, while adiabatic lattice density functional theory in the Bethe…
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…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
The variation with energy of the total cross section for elastic electron scattering from atoms of several elements is caused primarily by shape resonances corresponding to the formation of temporary negative ions. It is shown that such…
This paper considers the probability density and current distributions generated by a point-like, isotropic source of monoenergetic charges embedded into a uniform magnetic field environment. Electron sources of this kind have been realized…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
In this work we theoretically study steady state thermoelectric transport through a single-molecule junction with a long chain-like bridge. Electron transmission through the system is computed using a tight-binding model for the bridge. We…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
We apply a general method developed recently for the derivation of the diagonal representation of an arbitrary matrix valued quantum Hamiltonian to the particular case of Bloch electrons in an external electromagnetic field. We find the…
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…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…